Microfluidic methods of assaying molecule switching and devices for practicing the same

ABSTRACT

Microfluidic methods of assaying molecule switching are provided. Aspects of the methods include microfluidically separating a sample containing the molecule of interest and then employing the resultant separation pattern to determine a switching characteristic of the molecule. Also provided are microfluidic devices, as well as systems and kits that include the devices, which find use in practicing embodiments of the methods. The methods, devices, systems and kits find use in a variety of different applications, such as analytical and diagnostic assays.

CROSS-REFERENCE TO RELATED APPLICATION

Pursuant to 35 U.S.C. § 119 (e), this application claims priority to thefiling date of U.S. Provisional Patent Application Ser. No. 61/710,988filed on Oct. 8, 2012, the disclosure of which is herein incorporated byreference.

REFERENCE TO GOVERNMENT SUPPORT

This invention was made with government support under grant numberOD007294 awarded by the National Institutes of Health. The governmenthas certain rights in the invention.

INTRODUCTION

A variety of analytical techniques may be used to separate and detectspecific analytes in a given sample. A range of related immunoblottingmethods have enabled the identification and semi-quantitativecharacterization of e.g., DNA (Southern blot), RNA (northern blot),proteins (Western blot), and protein-protein interactions (far-westernblot); by coupling biomolecule separations and assays. For example,Western blotting can be used to detect proteins in a sample by using gelelectrophoresis to separate the proteins in the sample followed byprobing with antibodies specific for the target protein. In a typicalWestern blot, gel electrophoresis is used to separate native proteins by3-D structure or denatured proteins by the length of the polypeptide.The proteins are then transferred to a membrane (typicallynitrocellulose or PVDF), where they are probed (detected) usingantibodies specific to the target protein.

Conventional blotting techniques, as discussed above, may fall short ofperformance needs for applications that demand either high-throughputsample analysis or operation in resource poor settings. Blottingtechniques may require labor-intensive, time consuming, multi-stepprocedures carried out by a trained technician, and thus may beimpractical for use in a clinical setting. Furthermore, devices that areless expensive and easier to fabricate and operate are desired.

SUMMARY

Microfluidic methods of assaying molecule switching are provided.Aspects of the methods include microfluidically separating a samplecontaining the molecule of interest and then employing the resultantseparation pattern to determine a switching characteristic of themolecule. Also provided are microfluidic devices, as well as systems andkits that include the devices, which find use in practicing embodimentsof the methods. The methods, devices, systems and kits find use in avariety of different applications, such as analytical and diagnosticassays.

BRIEF DESCRIPTION OF THE FIGURES

FIG. 1A shows a workflow illustration for a method according toembodiments of the present disclosure. The method includes: (i)electrophoretic loading and IEF of a heterogeneous sample, (ii) UVphotoimmobilization of protein isoforms (grey bands), (iii)electrophoretic pH gradient washout, (iv) fluorescently labeled antibodyprobing of target antigen, and (v) washout of excess probe with specificfluorescence readout in an 80 min assay. FIG. 1B shows a photograph of amicrofluidic chip that includes 16 parallel separation media runningbetween 4 pairs of access wells. FIG. 1C shows images over time of IEFon CE540-labeled protein ladder mixed with wtGFP target in a singleseparation medium (red fluorescence imaging, nominal [ladder*]=0.38 mgml⁻¹, ladder is CytC: cytochrome C, RNase: ribonuclease A, LCL: lentillectin, Mb: myoglobin, CA: carbonic anhydrase, BLG: β-lactoglobulin,GOx: glucose oxidase, [GFP]=617 nM/16.7 μg ml⁻¹). FIG. 1D showsspectrally resolved pI markers co-focused in the same channel as in FIG.1C. Triplet peak pattern of wtGFP was detectable due to absorption inthe UV. FIG. 1E shows images over time of pH gradient washout after UVphotoactivation of the separation medium monitored via endogenous greenfluorescence of GFP, leaving gel-captured fraction behind. FIG. 1F showsimages over time of electrophoretic probing with 200 nM TexasRed-labeled pAb* to GFP.

FIG. 2 shows assays of wtGFP indicating a photoswitchable isoform,according to embodiments of the present disclosure. FIG. 2A shows agraph in which the top and middle traces are from the same experiment asFIGS. 1C-F, showing identical endogenous and probe relative fluorescencereadouts respectively after electrophoretic washout of excess probe(traces offset in y-axis by 0.2 and 0.3 RFU respectively for clarity);inset shows correspondence of signals. The peak labeled “†” is aphotoswitchable isoform with pI of 5.33. The bottom trace shows theimmobilized endogenous GFP fluorescence profile for 120 sec pre-exposureof isoforms to blue light via a 10× objective in the focused state. FIG.2B (bottom) shows an image of dynamic wtGFP pI 5.33 isoformphotoswitching in 10× field of view upon application of blue light indark, focused state (nominal [GFP]=617 nM). FIG. 2B (top) shows a graphof the switch-on of pI 5.33 isoform fluorescence indicating first-orderkinetics with a time constant of 420 msec.

FIG. 3 shows graphs indicating rapid photoimmobilization kinetics withhigh capture efficiency and weak pH dependence, according to embodimentsof the present disclosure. FIG. 3A shows a graph indicating defocusingof wtGFP (abrupt decrease in E_(IEF) from 300 V cm⁻¹ to 0 V cm⁻¹) withinverse square root dependence of pI 5 and 5.19 isoform resolution ontime (nominal [GFP]=617 nM). FIG. 3A (inset) shows GFP bands before andafter the defocusing period, showing a decrease in resolution bydiffusion. FIG. 3B shows a graph of capture efficiency η of 15 μM GFPunder non-focusing conditions against spot UV exposure time fit to

$\eta = {a\left( {b - e^{- \frac{t}{\tau}}} \right)}$with τ=5.5 s (n=4). Maximum η was ˜1.8% vs. <0.2% in BPMA− control gels.FIG. 3B (inset) shows images of the edges of separate microchannel UVexposure spots for several exposure times after washout of free GFP.FIG. 3C (top) shows a graph of ampholyte* η versus pH in BPMA+ and BPMA−separation media (η computed on the basis of the UV-exposed, refocusedfluorescence profiles, [ampholyte*]=0.025% w/v, grey envelopes are ±SD,n=4). Peaks caused by pI marker bleaching artifacts are marked by blackarrows. Native GFP* and PSA* efficiencies from separate chips are alsoshown (±SD, n=8 and 3 respectively). FIG. 3C (bottom) shows a graph ofcaptured ampholyte* SNR after gradient washout. The dotted linesdemarcate the approximate pH region of valid η data. FIG. 3D shows gelimages showing immobilized ampholyte* after electrophoretic washout,accompanied by focused-state pI markers.

FIG. 4 shows a linear separation medium calibration curve for purifiedPSA with inference of probe stoichiometry and the measurement of PSA incell lysate, according to embodiments of the present disclosure. FIG. 4Ashows images of a focused pI marker, primary (1°) and secondary (2°)fluorescent antibody probe signals for unlabeled purified PSA ([PSA]=500nM). Integrated signal over pH region is marked by brackets used toconstruct calibration curve in FIG. 4B. FIG. 4B shows a calibrationcurve in nominal [PSA]=1-500 nM range (0.033-16.5 μg ml⁻¹, [1°, 2°pAb*]=0.1 μM for [PSA]=1-20 nM, [1°, 2° pAb*]=1 μM for [PSA]=50-500 nM,n=4 for all points except 5 nM, n=2). FIG. 4C (bottom) shows a graph ofa comparison of signal after 1° and 2° probing for 500 nM PSA points.FIG. 4C (top) shows a graph of 2°:1° signal amplification ratio (dottedline marks baseline of nil 2° signal at 2°:1°=1, grey envelope was ±SD,n=4). FIG. 4D shows gel images of LAPC4 (PSA+) and DU145 (PSA−) 1° Ab*gel images (representative of 4 replicates per lysate, total proteinconcentration ˜1 mg ml⁻¹ each). The integrated signal over the pH regionmarked by brackets was used in ELISA comparison.

FIG. 5 shows microfluidic assays in recognition mapping mode forisoform-resolution probe screening, according to embodiments of thepresent disclosure. FIGS. 5A and 5B show gel images of CE540-labeledPSA* in focused, captured/washed and probed states for monoclonal (FIG.5A) and polyclonal Ab* (FIG. 5B) (all gel images were adjusted foridentical contrast, [PSA*]=500 nM, [mAb*, pAb*]=1 μM).Electrophoretically washed data showed a lack of contribution to probesignals by immobilized PSA* detected on the same spectral channel. FIG.5C shows a graph of 1° Ab* readouts aligned to corresponding focusedPSA* traces. FIG. 5D shows a graph of probed:focused signal ratiosadjusted by GFP capture efficiency (grey envelopes are ±SD, n=8 for eachof mAb* and pAb* sets). FIG. 5E shows a graph of the ratio of pAb*:mAb*data from FIG. 5D.

FIG. 6 shows a reaction scheme of a light-activated covalent bondingreaction between the carbonyl functional groups of a benzophenonemethacrylamide (BPMA) monomer and target polypeptide, according toembodiments of the present disclosure.

FIG. 7 shows a molecular model of a reaction scheme of a light-activatedcovalent bonding reaction between the carbonyl functional groups of abenzophenone methacrylamide (BPMA) monomer and target polypeptide,according to embodiments of the present disclosure.

FIG. 8 shows a graph of separation resolution of analyte pairs underfocusing conditions for the 8 pI markers and 3 GFP isoforms presented inFIG. 1D (55 total comparisons), according to embodiments of the presentdisclosure. A threshold of R_(s)=1 yielded a minimum separable pIdifference of 0.15 via linear regression.

FIG. 9 shows gel images and a graph indicating that colocalizedampholyte* species and pI markers yielded enhanced photobleaching,according to embodiments of the present disclosure. FIG. 9A shows gelimages of the effect of 10 sec flood UV exposure on ampholyte* profilein the focused state prior to washout. pI markers increased localampholyte* bleaching (grey and black arrows). FIG. 9B shows a graph ofampholyte* signal retained after UV exposure. Troughs in pI markerregions are marked by black arrows. Higher overall bleaching occurred inthe BPMA+ separation medium, which may be due to side reactions betweenampholyte* radicals and other reactive species generated upon BPMAphotoactivation.

FIG. 10 shows graphs of microplate experiments that show the denaturingeffect of GFP labeling and allow extraction of ε_(pHw,pHf). FIG. 10(top), solid lines are microplate green fluorescence data for analytes(1 μM each) in 50 μl aliquots of loading buffers titrated to themeasured pH values shown with 2M HCl or NaOH. Data points at pH 9.9 arefor washout buffer (wb) samples (see Table 1 for buffer compositions).ε_(pHw=9.9,pHf≈5) for GFP was approximated via the ratio of fluorescencevalues at the points indicated by short arrows. FIG. 10 (bottom) shows agraph of the corresponding red fluorescence values for each analyte,which shows a negligible dependence of CE540 fluorescence on pH for alllabeled species.

FIG. 11 shows graphs indicating CE540-labeled GFP exists as native(green+, red+) and denatured (green−, red+) sub-populations. The graphshows aligned relative fluorescence data from sequential imaging ongreen and red spectral channels for GFP* focused at 300 V cm⁻¹ in asingle separation medium (nominal [GFP*]=617 nM). The red fluorescencereadout was dominated by the denatured population, presenting as adiffuse set of bands with rough correspondence to those of the nativeGFP* population (green fluorescence readout). The canonical 3-bandstructure observed for the native GFP* population was similar to that ofunlabeled GFP (see FIG. 2A).

FIG. 12 shows gel images of embodiments of the microfluidic devices andcompanion slab-gel IEF assays. FIG. 12A shows gel images of a comparisonof purified PSA and GFP readouts in the subject microfluidic device toNovex slab gel (GFP visible in pI marker set). FIG. 12B shows gel magesof a PSA isoform pattern in a custom slab gel that agrees with majorband assignments in the subject microfluidic device (gel buffercompositions here were identical to those in the subject microfluidicdevice).

FIG. 13 shows experiments of the integration of microfluidic nativesize-based separation and immunoprobing in a microfluidic deviceaccording to embodiments of the present disclosure. Separation of amixture of fluorescent proteins (top trace) was performed in the gelfrom left to right from an injection zone at a cross-channel T chip.Photocapture was initiated via application of UV light. Washout ofunbound protein and subsequent immunoprobing for ovalbumin (OVA*) wasperformed in situ, with specific fluorescent readout (bottom trace).

FIG. 14 shows an experiment performed similarly to FIG. 13, except withreduced and denatured sample (e.g., SDS-PAGE), according to embodimentsof the present disclosure. Sample preparation with SDS, DTT reducingagent and heating was performed in the vein of traditional LaemmliSDS-PAGE. In-situ immunoprobing (red) was then performed for ovalbuminafter capture of separated species (green) onto the separation mediumand washout of excess SDS detergent. This experiment demonstratesSDS-PAGE with immunoprobing (typically referred to as “Westernblotting”) performed in an integrated microfluidic device.

FIG. 15 shows gel images of transient isotachophoretic stacking ofproteins induced by a step change in channel pH, which manipulated themobility of a glycine trailing ion similar to traditional LaemmliSDS-PAGE, according to embodiments of the present disclosure. Theinitial diffuse sample zone was stacked in the low pH region beforeentering a higher pH region in which the glycine trailing ion overtookthe protein bands, causing them to separate by size.

FIG. 16 shows gel images of single-channel SDS-PAGE with stacking bytransient ITP (frames 1 and 2 at left), separation of proteins by size(frame 3 and continuous plot at center), and probing for multipleanalytes in separate devices following immobilization (antibodyfluorescence data at right), according to embodiments of the presentdisclosure. β-gal is β-galactosidase.

FIG. 17 shows a graph of separation of a benchmark protein ladder bySDS-PAGE, showing the expected log-linear relationship, according toembodiments of the present disclosure.

FIG. 18 shows experiments for rapid, multiplexed micro-Western blottingin a single microchannel, according to embodiments of the presentdisclosure. FIG. 18A shows a schematic of a scalable-throughput, 10-60min microfluidic method that includes: (i) analyte stacking andSDS-PAGE; (ii) band capture onto the separation medium; (iii) removal ofSDS by brief electrophoretic washing; (iv) electrophoretic introductionof fluorescently-labeled primary and (optionally) secondary detectionantibodies specific to target; and (v) washout of excess probe.Ultra-rapid assay readout was also enabled by dynamic probe imaging.FIG. 18B shows a continuous gel image over time of SDS-PAGE offluorescently-labeled six protein ladder, completed in 60 s (4×magnification; band weights are 155, 98, 63, 40, 32, and 21 kDa).Channel aspect ratios were adjusted to produce gel-like images (seedimensions). (i) Transient isotachophoresis. (ii) SDS-PAGE. FIG. 18Cshows fluorescence images and intensity for four ladder proteinsphotoimmobilized after SDS-PAGE (1 μM each, weights in kDa); before andafter washout of uncaptured protein. At right, capture efficiency ofbovine serum albumin (BSA, ±SD, n=3) for separation media fabricatedchemically or photochemically. FIG. 18D shows a multiplexedmicro-Western blot readout (red) in 40 min total assay times usingprimary antibodies for (i) ovalbumin (OVA), (ii) β-galactosidase(β-gal), OVA and trypsin inhibitor (TI), and (iii) β-gal, gp120, OVA,prostate specific antigen (PSA, 34 kDa) and TI (gp120, 200 nM; othersantigens, 1 μM).

FIG. 19 shows a micro-Western blot for quantitative, rapid, andhigh-sensitivity readout modes, according to embodiments of the presentdisclosure. FIG. 19A shows a schematic of modular interfacing ofmicrochips with a scalable electrode array. FIG. 19B shows 54 parallelmicro-Western blots (18 samples in triplicate) of the four proteinfluorescent ladder probed for ovalbumin (OVA) and β-galactosidase(β-gal) targets (1 μM each) with red fluorescent primary antibodies in40 min total assay time. At top, total injected (inj.) fluorescence onweight marker spectral channel at the end of the ITP phase of SDS-PAGEacted as loading control. FIG. 19C shows fluorescence micrographs andplot of signal-to-noise ratio (SNR, ±SD, n=3) for electrophoreticintroduction of red fluorescent primary antibody (Ab*) to OVA band at 4min total assay time (arrow). FIG. 19D shows further probing ofmicro-Western blots from FIG. 19B with 10 nM alkaline phosphatase(AP)-conjugated donkey anti-goat IgG for specific amplification of theβ-gal band. Electrophoretic introduction of 300 μM DiFMUP phosphatasesubstrate led to blue DiFMU product signal development upon stoppedelectric field. Dynamic fluorescence imaging compared β-gal peak SNR onred (primary antibody) and blue (DiFMU) fluorescence channels duringthis stopped field period.

FIG. 20 shows experiments for the validation of micro-Western blottingfor lysates and purified proteins, according to embodiments of thepresent disclosure. FIG. 20A shows gel images of a 60 min micro-Westernblot of 0.5 mg/ml transfected 293T lysate probed for NFκB with primaryand fluorescently labeled secondary antibodies (red). Untransfectednegative control lysate and loading controls (GAPDH and total injectedfluorescence, inj.) were included. At right, the correspondingconventional 6-8 hr western blot readouts are shown for visualcomparison. The conventional blot dimensions, “footprint” surface areawas 800-fold larger than the micro-Western. FIG. 20B shows gel images of40 min micro-Western blots of purified human immunodeficiency virus(HIV) proteins (reverse transcriptase, RT, 200 nM; gp120, 200 nM; p24, 1μM) after probing targets with fluorescently labeled primary antibodies(red). FIG. 20C shows a graph of standard curves for NFκB and gp120(±SD, n=3) constructed from the peak areas of the bands indicated byarrows in FIGS. 20A and 20B. gp120 is over the 5-200 nM range; NFκB isover 1:1 to 1:128 lysate dilution.

FIG. 21 shows 60 min micro-Western blots for human immunodeficiencyvirus (HIV) antibody detection in human sera, according to embodimentsof the present disclosure. FIG. 21A shows a schematic of a conventionalconfirmatory HIV diagnostic assay. FIG. 21B shows gel images of thereactivity of 1:100-diluted strongly reactive (++), weakly reactive (+)and non-reactive control (−) human sera to gp120 (200 nM) and p24 (1 μM)“bait” proteins revealed by fluorescently-labeled secondary antibody tohuman IgG (red). At right, the conventional 6-1812 hr HIV western blot,with gp120- and p24-reactive bands indicated by arrows. The conventionalblot used whole HIV lysate, whereas the micro-Western used specific HIVantigens, accounting for the additional reactive bands visible in theconventional blot.

FIG. 22 shows immunoprobed isoelectric focusing, which allows dynamicand immunoreactivity-verified monitoring of GFP isoform dynamics duringreversible photobleaching, according to embodiments of the presentdisclosure. FIG. 22(A) shows a schematic of reversible photobleachingupon UV illumination, which created dark GFP isoforms with increased plsrelative to their bright “parents”. FIG. 22(B) shows a microfluidic chipwith three parallel channels between each pair of access wells. Dynamicisoelectric photoswitching processes were monitored in real time, orisoforms were captured to the gel matrix and probed in situ withfluorescently labeled anti-GFP antibody (Ab*). FIG. 22(C) shows aschematic of avGFP chromophore and proton wire dynamics. Hydrogen bondnetworks allow proton exchange of the chromophore pocket with theexternal solvent. Glu222 was involved in excited state proton transfer(ESPT) with the chromophore Tyr66. The E222G mutation in acGFP inhibitedESPT and proton exchange with the internal wire. The dependence ofreversible photobleaching magnitude on pH indicated involvement of atitratable residue, X, in the chromophore vicinity that affectedchromophore protonation state by hydrogen bonding.

FIG. 23 shows probed isoelectric focusing of avGFP and acGFP, whichshows the base-shifted reversibly photobleached isoforms, according toembodiments of the present disclosure. FIG. 23(A) shows static gelfluorescence images and electropherograms of immobilized avGFP isoforms(bright: α, β, γ; dark: α′ and β′; γ′ is below the assay limit ofdetection) within the microchannel (black; excitation 445-495 nm,emission 508-583 nm) after focusing under—top: nil light exposureconditions, bottom: 150 ms pre-exposure to 100% UV (270 mW cm⁻², 300-380nm). Isoform capture was initiated immediately after the indicatedpre-exposure protocol by 15 s UV irradiation of the gel undernon-focusing conditions. Red fluorescence (excitation 525-555 nm,emission>575 nm) gel images and electropherograms were producedfollowing pH gradient washout and gel probing with 600 nM TexasRed-labeled anti-GFP antibody for immobilized isoforms. The fluorescenceof captured dark isoforms (α′ and β′) was switched on during imagingunder blue illumination. FIG. 23(B) shoes the corresponding micrographsand electropherograms for immobilized acGFP isoforms (bright: δ, ε, ζ;dark: δ′, ε′ and ζ′) probed with the same anti-GFP antibody.

FIG. 24 shows real-time observation of isoelectric point photoswitchingin avGFP, according to embodiments of the present disclosure. FIGS.24(A-C) show log-transformed fluorescence micrographs corrected forcathodic pH gradient drift showing dynamic isoelectric point evolutionof avGFP isoforms during isoelectric focusing over time (100 ms streamedexposures, E=300 V cm⁻¹). Initial and final electropherograms in linearrelative fluorescence units accompany each timelapse micrograph. Thethree panels show typical behavior upon applying a sequence ofmicrochannel exposure conditions: FIG. 24(A) Nil-to-blue light exposure;FIG. 24(B) 100% UV exposure (excitation 300-380 nm, emission>410 nm);and FIG. 24(C) Blue light exposure. Delay between micrographs due tofilter cube exchange was ˜2 s.

FIG. 25 shows isoelectric photoswitching kinetics, according toembodiments of the present disclosure. FIG. 25(A) shows fluorescencephotoswitching in avGFP and acGFP. Ten consecutive illumination cyclesof 100% UV (1 s per cycle) and blue light (5 s per cycle) were conductedvia 10× objective and total isoform fluorescence plotted over time for10 ms frames. FIG. 25(B) shows fast reversible bleaching of isoformsunder UV illumination. Left: Dark isoforms of avGFP were generated bypre-exposure of bands to 100% UV light for the indicated exposure timesy, followed by a focusing equilibration period of 7 s under nilillumination. Focusing field was then halted and dark isoforms convertedto the bright state by 3 s blue light exposure and quantified bymeasuring peak areas. Electropherograms showed an increase in darkisoform (α′ and β′) representation as a function of UV pre-illuminationperiod. Right: Growth of dark state isoform peak areas in pI 5.25-5.6range were determined from electropherogram data at left (black) andinferred by direct observation of bleaching under 100% UV (purple, fromthe first exposure cycle of (A)), both fit to RFU=a(1−e^(−t/τ))+b. FIG.25(C) shows slow isoform fluorescence recovery under nil illumination.Left: Dark isoforms of avGFP were generated by 10 s pre-exposure ofbands to 100% UV light via 10× objective, followed by a nil illuminationperiod z of between 10 and 170 s. The focusing field was then halted andremaining dark isoforms were converted to the bright state by 3 s bluelight exposure. Electropherograms showed decay in the representation ofdark isoform (α′ and β′) peak areas in the pI 5.25-5.6 range as afunction of nil illumination period. Right: Dark isoform peak areas fitto a single exponential of the form RFU=RFU_(max)e^(−t/τ) (±SD, n=3,error bar heights smaller than marker size).

FIG. 26 shows two-state convection-diffusion-reaction model predictsfocusing dynamics during perturbation of avGFP with UV light, accordingto embodiments of the present disclosure. FIG. 26(A) shows, at left, asketch of concentration distributions from 1D model of focusing ofbright (β) and dark (β′) states of the major avGFP isoform over a rangeof interconversion rates; x-axes are pI 4.8-5.5, y-axes are arbitraryfluorescence units. κ/Pe compares reaction to focusing speeds, governingthe observed morphology of the β peak during focusing. Concentrationdistributions of the bright and dark states can be distinct (κ/Pe<1) oroverlapping (κ/Pe>1) depending on the UV intensity, even for the sameequilibrium constant γ. Right hand column, least-squares fits of modeldistributions of β to experiment data for the indicated UV intensities.Fits from 10%-100% UV were global optima, while that at 2% assumed anaverage γ value from the other fits (square brackets and dashed linesdenote this here and in FIGS. 26(B) and (C)). FIG. 26(B) showsinterconversion rates between β and β′ states and their ratio, γ, fromfits in (A). FIG. 26(C) shows intensity plots of pI mean and standarddeviation for the sum of β and β′ distributions. Interconversion ratesdetermined from experimental data in (B) are overlayed. Best-fit slopeof 0.94 reflects approximately constant γ and mean pI across the UVrange.

DETAILED DESCRIPTION

Microfluidic methods of assaying molecule switching are provided.Aspects of the methods include microfluidically separating a samplecontaining the molecule of interest and then employing the resultantseparation pattern to determine a switching characteristic of themolecule. Also provided are microfluidic devices, as well as systems andkits that include the devices, which find use in practicing embodimentsof the methods. The methods, devices, systems and kits find use in avariety of different applications, such as analytical and diagnosticassays.

Microfluidic Devices

Aspects of the present disclosure include microfluidic devices forseparating constituents of a fluid sample. A “microfluidic device” isdevice that is configured to control and manipulate fluids geometricallyconstrained to a small scale (e.g., sub-millimeter). Embodiments of themicrofluidic devices include an elongated flow path and a separationmedium. The separation medium may be configured to separate constituentsin a sample from each other. In certain embodiments, the microfluidicdevice is configured to perform a method of assaying molecule switchingas described in more detail below. For example, the microfluidic devicemay be configured to microfluidically separate a sample that includes amolecule to obtain a separation pattern, and determine a switchingcharacteristic of the molecule from the switching pattern. In someinstances, the separation medium may include functional groups thatcovalently bond to one or more constituents of interest in theseparation medium upon application of an applied stimulus. The separatedconstituents may then be detected. Additional details about theseparation medium are discussed below.

Separation Medium

In certain embodiments, the microfluidic devices include a separationmedium. The separation medium may be configured to separate constituentsof a sample from each other. In some cases, the separation medium isconfigured to separate constituents in a sample based on the physicalproperties of the constituents. For example, the separation medium maybe configured to separate the constituents in the sample based on themolecular mass, size, charge (e.g., charge to mass ratio), isoelectricpoint, etc. of the constituents.

In certain instances, the separation medium is configured to separatethe constituents in the sample based on the size and charge of theconstituents. The separation medium may be configured to separate theconstituents in the sample into distinct detectable bands ofconstituents. By “band” is meant a distinct detectable region where theconcentration of a constituent is significantly higher than thesurrounding regions. Each band of constituent may include a singleconstituent or several constituents, where each constituent in a singleband of constituents has substantially similar physical properties, asdescribed above.

In certain embodiments, the separation medium is configured to separatethe constituents in a sample as the sample traverses the separationmedium. In some cases, the separation medium is configured to separatethe constituents in the sample as the sample flows through theseparation medium. Aspects of the separation medium include that theseparation medium has a directional axis. In some instances, thedirectional axis is oriented in the direction the sample travels as thesample traverses the separation medium. In some embodiments, thedirectional axis of the separation medium is aligned with the length ofthe separation medium. In these embodiments, the sample traverses theseparation medium along the length of the separation medium. In somecases, the length of the separation medium is greater than the width ofthe separation medium, such as 2 times, 3 times, 4 times, 5 times, 10times, 25 times, 50 times, 75 times, 100 times, 125 times, 150 times,175 times, or 200 times or more the width of the separation medium.

In some instances, the separation medium is defined by a region of themicrofluidic device that includes the separation medium. For example,the microfluidic device may include an elongated flow path. Theelongated flow path may include the separation medium. For instance, themicrofluidic device may include a channel (e.g., a microfluidicchannel). The channel may include the separation medium. The separationmedium may be included in the channel, such that a sample traverses theseparation medium as the sample flows through the channel. In someinstances, the length of the elongated flow path is greater than thewidth of the elongated flow path, such as 2 times, 3 times, 4 times, 5times, 10 times, 25 times, 50 times, 75 times, 100 times, 125 times, 150times, 175 times, or 200 or more times the width of the elongated flowpath.

In certain embodiments, the separation medium includes a polymer, suchas a polymeric gel. The polymeric gel may be a gel suitable for gelelectrophoresis. The polymeric gel may include, but is not limited to, apolyacrylamide gel (e.g., methacrylamide gel), an agarose gel, and thelike. The resolution of the separation medium may depend on variousfactors, such as, but not limited to, pore size, total polymer content(e.g., total acrylamide content), concentration of cross-linker, appliedelectric field, assay time, and the like. For instance, the resolutionof the separation medium may depend on the pore size of the separationmedium. In some cases, the pore size depends on the total polymercontent of the separation medium and/or the concentration ofcross-linker in the separation medium. In certain instances, theseparation medium is configured to resolve analytes with molecular massdifferences of 50,000 Da or less, or 25,000 Da or less, or 10,000 Da orless, such as 7,000 Da or less, including 5,000 Da or less, or 2,000 Daor less, or 1,000 Da or less, for example 500 Da or less, or 100 Da orless. In some cases, the separation medium may include a polyacrylamidegel that has a total acrylamide content, T (T=total concentration ofacrylamide and bisacrylamide monomer), ranging from 1% to 20%, such asfrom 3% to 15%, including from 5% to 10%. In some instances, theseparation medium has a total acrylamide content of 7.5%. In certaincases, the separation medium has a total acrylamide content of 6%.

In certain embodiments, the separation medium is configured to be formedfrom precursor moieties. For example, the separation medium may be a gel(e.g., a polyacrylamide gel) formed form gel precursors (e.g.,polyacrylamide gel precursors, such as polyacrylamide gel monomers). Theprecursor moieties may be configured to react to form the separationmedium. For instance, the gel precursors may be configured to react witheach other to form the polyacrylamide gel separation medium. Thereaction between the gel precursors may be activated by any suitableprotocol, such as, but not limited to, chemical activation, lightactivation, etc. In some embodiments, the gel precursors are configuredto be activated chemically, for example by contacting the gel precursorswith an activation agent, such as, but not limited to, a peroxide. Insome embodiments, the gel precursors are configured to be activated bylight (i.e., photo-activated), for instance by contacting the gelprecursors with light. The light may be of any wavelength suitable foractivating the formation of the separation medium, and in some instancesmay have a wavelength associated with blue light in the visiblespectrum. For example, the light used to activate formation of theseparation medium may have a wavelength ranging from 400 nm to 500 nm,such as from 410 nm to 490 nm, including from 420 nm to 480 nm, or from430 nm to 480 nm, or from 440 nm to 480 nm, or from 450 nm to 480 nm, orfrom 460 nm to 480 nm, or from 465 nm to 475 nm. In certain cases, thelight used to activate formation of the separation medium has awavelength ranging from 465 to 475 nm. In some instances, the light usedto activate formation of the separation medium has a wavelength of 470nm.

In certain embodiments, the separation medium includes a buffer. Thebuffer may be any convenient buffer used for gel electrophoresis. Incertain embodiments, the buffer is a Tris buffer. In certainembodiments, the separation medium includes a buffer, such as aTris-glycine buffer. For example, the buffer may include a mixture ofTris and glycine.

In some cases, the buffer includes a detergent. In certain instances,the detergent is configured to provide analytes in the sample withsubstantially similar charge-to-mass ratios. Analytes with substantiallysimilar charge-to-mass ratios may facilitate the separation of theanalytes into one or more bands in the separation medium based on themolecular masses of the analytes in the sample. In certain cases, thedetergent is anionic detergent configured to provide analytes in thesample with a charge, such as a negative charge. For example, thedetergent may be an anionic detergent, such as, but not limited to,sodium dodecyl sulfate (SDS).

In certain embodiments, the separation medium is configured to separatethe constituents in the sample based on the isoelectric point (pI) ofthe constituents (e.g., isoelectric focusing, IEF). In some cases, theseparation medium includes a polymeric gel as described above. Forexample, the polymeric gel may include a polyacrylamide gel, an agarosegel, and the like. In certain instances, the polymeric gel includes a pHgradient, which, in some embodiments, is co-polymerized with thepolymeric gel. In embodiments where the pH gradient is co-polymerizedwith the polymeric gel, the pH gradient may be substantially immobilizedresulting in a separation medium having an immobilized pH gradient. Incertain instances, the pH gradient includes a weak acid or a weak base(e.g., Immobilines), ampholytes, or the like.

In certain embodiments, the separation medium is configured to separateconstituents in a sample based on size. For example, in some cases, theseparation medium includes a polymeric gel having a pore size gradient.The pore size gradient may decrease along the directional axis of theseparation medium. For example, the pore size gradient may have a poresize that decreases along the directional axis of the separation medium,such that a sample traversing the separation medium encountersprogressively smaller and smaller pore sizes in the separation medium.As constituents in the sample traverse the pore size gradient, theconstituents in the sample may be separated based on size. For example,larger constituents in the sample may be retained in the separationmedium more readily than smaller constituents, which are able totraverse greater distances through the decreasing pore size gradient.

In some cases, the pore size of the separation medium depends on thetotal polymer content of the separation medium and/or the concentrationof cross-linker in the separation medium. In certain instances, theseparation medium pore size sufficient to resolve analytes withmolecular mass differences of 50,000 Da or less, or 25,000 Da or less,or 10,000 Da or less, such as 7,000 Da or less, including 5,000 Da orless, or 2,000 Da or less, or 1,000 Da or less, for example 500 Da orless, or 100 Da or less. In some cases, the separation medium mayinclude a polyacrylamide gel that has a pore size that depends on thetotal acrylamide content, T (T=total concentration of acrylamide andbisacrylamide monomer), where the total acrylamide content ranges from1% to 20%, such as from 3% to 15%, including from 5% to 10%. In someinstances, the separation medium has pore size defined by a totalacrylamide content of 7.5%. In certain cases, the separation medium hasa pore size defined by a total acrylamide content of 6%.

In certain embodiments, the support (e.g., separation medium) isconfigured to covalently bond to the constituents of interest. Thecovalent bond may be formed upon application of an applied stimulus. Forexample, the applied stimulus may include electromagnetic radiation,such as light. In some cases, the light is ultraviolet (UV) light. Insome instances, the light used to covalently bond the constituents ofinterest to the separation medium has a wavelength ranging from 10 nm to400 nm, such as from 50 nm to 400 nm, including from 100 nm to 400 nm,or from 150 nm to 400 nm, or from 200 nm to 400 nm, or from 250 nm to400 nm, or from 300 nm to 400 nm, or form 325 nm to 375 nm, or from 350nm to 365 nm. In certain cases, the light has a wavelength ranging from350 to 365 nm.

In certain embodiments, the light used to covalently bond theconstituents of interest to the separation medium has a wavelengthdifferent from the light used to activate formation of the separationmedium. For example, as described above, the light used to activateformation of the separation medium may have a wavelength of blue lightin the visible spectrum. As described above, the light used tocovalently bond the constituents of interest to the separation mediummay have a wavelength of UV light. As such, in certain embodiments, theseparation medium is configured to be formed upon application of a firstwavelength of light, and configured to covalently bond the constituentsof interest upon application of a second wavelength of light. The firstand second wavelengths of light may be blue light and UV light,respectively, as described above.

In some cases, the separation medium includes functional groups thatcovalently bond to the one or more constituents of interest. Forexample, the constituents of interest may be an analyte of interest,such as, but not limited to, a protein, a peptide, and the like. Thefunctional groups may include functional groups that are activated uponapplication of an applied stimulus, such as electromagnetic radiation(e.g., light) as described above. As such, in certain instances, thefunctional groups are light-activatable functional groups. Uponapplication of light, the light-activatable functional groups may form areactive species capable of forming covalent bonds, such as a radicalalkyl intermediate. Examples of functional groups that may covalentlybond to the constituents of interest upon application of an appliedstimulus (e.g., light) include, but are not limited to, benzophenonegroups, and the like. Once activated by the applied stimulus, thefunctional group may bond to the constituent of interest (e.g., proteinor peptide) forming a covalent bond between the separation medium andthe constituent of interest. For example, the functional group may forma carbon-carbon bond between the functional group and the constituent ofinterest.

In some embodiments, the functional groups are co-polymerized with theseparation medium. For example, the functional groups may include alinker group that is attached to the separation medium. The functionalgroup may be bound to the linker group at a first end of the linkergroup, and a second end of the linker group may be bound to theseparation medium, thereby indirectly bonding the functional group tothe separation medium. In some instances, the second end of the linkergroup, which is bound to the separation medium, includes a co-monomer,such as, but not limited to, an acrylamide co-monomer, and the like. Insome embodiments, the second end of the linker group includes amethacrylamide co-monomer. In certain cases, the functional group is abenzophenone functional group and the linker group includes aco-monomer, such as an acrylamide co-monomer. For example, thefunctional group (including the linker group) may beN-(3-[(4-benzoylphenyl)formamido]propyl) methacrylamide (also known asBPMA or BPMAC). As described above, the linker group may have a firstend bound to the functional group, and a second end bound to theseparation medium. In some instances, the middle portion of the linkergroup between the first and second ends includes an aliphatic group,such as, but not limited to, a C₁-C₁₀ alkyl group. In certain cases, themiddle portion of the linker group includes a lower alkyl group (e.g., aC₁-C₆ alkyl group). For instance, the middle portion of the linker groupmay include a propyl group.

In certain embodiments, the separation medium is configured to bind toconstituents in a sample at a minimum capture efficiency. The captureefficiency is the percentage of constituents in the sample that arebound by the separation medium. In some instances, the captureefficiency, η, is the ratio of fluorescence measured after gradientwashout (AFU_(w)) to the fluorescence during focusing (AFU_(f)),corrected by a factor ε to account for the anticipated influence of pHon the species fluorescence signal. In certain embodiments, theseparation medium is configured to have a capture efficiency of 1% ormore, such as 5% or more, including 10% or more, or 20% or more, or 30%or more, or 40% or more, or 50% or more, or 60% or more, or 70% or more,or 80% or more, or 90% or more, or 95% or more. In some instances, theseparation medium has a capture efficiency of 75% or more.

Further Aspects of Embodiments of the Microfluidic Devices

Aspects of the microfluidic devices include embodiments where themicrofluidic device is configured to subject a sample to a flow field.By “flow field” is meant a region where components traverse the regionin substantially the same direction. For example, a flow field mayinclude a region where mobile components move through a medium insubstantially the same direction. A flow field may include a medium,such as a separation medium, a loading medium, etc., where components,such as buffers, analytes, reagents, etc., move through the medium insubstantially the same direction. A flow field may be induced by anapplied electric field, a pressure differential, electroosmosis, and thelike. In some embodiments, flow field may be directionally distinct. Forexample, the flow field may be aligned with the directional axis of theseparation medium. The flow field may be configured to direct the sampleor constituents (e.g., analytes) through the elongated flow pathcontaining the separation medium.

In certain embodiments, the microfluidic device is configured to subjecta sample to an electric field. The electric field may facilitate themovement of the sample through the microfluidic device (e.g.,electrokinetic transfer of the sample from one region of themicrofluidic device to another region of the microfluidic device). Theelectric field may also facilitate the separation of the analytes in thesample by electrophoresis (e.g., polyacrylamide gel electrophoresis(PAGE), SDS-PAGE, isoelectric focusing, etc.), as described above.

For instance, the electric field may be configured to direct theanalytes in a sample through the separation medium of the microfluidicdevice. The electric field may be configured to facilitate theseparation of the analytes in a sample based on the physical propertiesof the analytes. For example, the electric field may be configured tofacilitate the separation of the analytes in the sample based on themolecular mass, size, charge (e.g., charge to mass ratio), isoelectricpoint, etc. of the analytes. In certain instances, the electric field isconfigured to facilitate the separation of the analytes in the samplebased on the molecular mass of the analytes. In other embodiments, theelectric field is configured to facilitate separation of the analytes inthe sample based on the isoelectric point (pI) of the analytes.

In some embodiments, the electric field may be directionally distinct.For example, the electric field may be aligned with the directional axisof the separation medium. The electric field may be configured to directthe sample or analytes through the separation medium along thedirectional axis of the separation medium.

In certain embodiments, the microfluidic device includes one or moreelectric field generators configured to generate an electric field. Theelectric field generator may be configured to apply an electric field tovarious regions of the microfluidic device, such as one or more of theseparation medium, the loading medium, and the like. The electric fieldgenerators may be configured to electrokinetically transport theanalytes and components in a sample through the various media in themicrofluidic device. In certain instances, the electric field generatorsmay be proximal to the microfluidic device, such as arranged on themicrofluidic device. In some cases, the electric field generators arepositioned a distance away from the microfluidic device. For example,the electric field generators may be incorporated into a system for usewith the microfluidic device, as described in more detail below.

Embodiments of the microfluidic device may be made of any suitablematerial that is compatible with the assay conditions, samples, buffers,reagents, etc. used in the microfluidic device. In some cases, themicrofluidic device is made of a material that is substantially inert(e.g., does not degrade or react) with respect to the samples, buffers,reagents, etc. used in the subject microfluidic device and methods. Forinstance, the microfluidic device may be made of materials, such as, butnot limited to, glass, quartz, polymers, elastomers, paper, combinationsthereof, and the like.

In some instances, the microfluidic device includes one or more sampleinput ports. The sample input port may be configured to allow a sampleto be introduced into the microfluidic device. The sample input port maybe in fluid communication with the separation medium. In some instances,the sample input port is in fluid communication with the upstream end ofthe separation medium. The sample input port may further include astructure configured to prevent fluid from exiting the sample inputport. For example, the sample input port may include a cap, valve, seal,etc. that may be, for instance, punctured or opened to allow theintroduction of a sample into the microfluidic device, and thenre-sealed or closed to substantially prevent fluid, including the sampleand/or buffer, from exiting the sample input port.

In certain embodiments, the microfluidic device is substantiallytransparent. By “transparent” is meant that a substance allows visiblelight to pass through the substance. In some embodiments, a transparentmicrofluidic device facilitates application of an applied stimulus(e.g., electromagnetic radiation, such as light, including visiblelight, UV light, etc.) to the separation medium. In certain cases, atransparent microfluidic device facilitates detection of analytes boundto the separation medium, for example analytes that include a detectablelabel, such as a fluorescent label.

In some aspects, the separation medium is provided in an elongated flowpath, as illustrated in FIG. 1. In these embodiments, the microfluidicdevice includes a channel, such as a microfluidic channel. The channelmay include the separation medium as described above. In certainembodiments, the elongated flow path includes an interior volume definedby the sides of the elongated flow path. For example, the elongated flowpath may be a channel (e.g., a microfluidic channel), which may definean interior volume of the channel. In certain instances, the separationmedium is provided in the interior volume of the elongated flow path.For instance, the separation medium may be provided in substantially theentire interior volume of the functional region of the elongated flowpath. The functional region of the elongated flow path is the regionused for separation and detection of the sample constituents and may notinclude other regions of the elongated flow path, e.g., for sampleloading, buffer reservoirs, microfluidic fluid conduits, etc. Asdescribed above, the separation medium may be provided in substantiallythe entire interior volume of the functional region of the elongatedflow path, such that the separation medium substantially fills the widthof the interior volume of the elongated flow path. In these embodiments,the separation medium substantially fills the interior volume of theelongated flow path, such that there are no significant voids in theinterior volume that do not include the separation medium. For instance,in these embodiments, the separation medium is not a coating on theinterior surface of the elongated flow path, but rather the separationmedium substantially fills the interior volume of the elongated flowpath.

In addition to the separation medium, the microfluidic device may alsoinclude a loading medium. The loading medium may be in fluidcommunication with the separation medium. In some instances, the loadingmedium is in direct physical contact with the separation medium. Forexample, the loading medium may be bound to the separation medium, suchas contiguously photopatterned with the separation medium. The loadingmedium may be positioned such that the sample contacts the loadingmedium before contacting the separation medium. For example, the loadingmedium may be positioned upstream from the separation medium in theelongated flow path. In certain embodiments, the loading mediumfacilitates contacting a sample with the separation medium. Forinstance, the loading medium may be configured to concentrate the samplebefore the sample contacts the separation medium. In certainembodiments, the loading medium may include two or more regions thathave different physical and/or chemical properties. The loading mediummay include a loading region and a stacking region. The loading mediummay be configured to include a loading region upstream from a stackingregion.

In certain embodiments, the loading medium includes a polymer, such as apolymeric gel. The polymeric gel may be a gel suitable for gelelectrophoresis. The polymeric gel may include, but is not limited to, apolyacrylamide gel, an agarose gel, and the like. In some cases, theloading region includes a polymeric gel with a large pore size. Forexample, the loading region may include a polyacrylamide gel that has atotal acrylamide content of 5% or less, such as 4% or less, including 3%or less, or 2% or less. In some instances, the loading region has atotal acrylamide content of 3%.

In some cases, the stacking region of the loading medium may beconfigured to concentrate the sample before the sample contacts theseparation medium. The stacking region may include a polymeric gel witha smaller pore size than the loading region. For example, the stackingregion may include a polyacrylamide gel that has a total acrylamidecontent of ranging from 5% to 10%, such as from 5% to 9%, including from5% to 8%, or from 6% to 8%. In some cases, the stacking region has atotal acrylamide content of 7.5%. In some instances, the stacking regionhas a total acrylamide content of 6%. The smaller pore size of thestacking region, as compared to the loading medium, may slow theelectrophoretic movement of the sample through the stacking region, thusconcentrating the sample before it contacts the separation medium.

In certain instances, the channel contains the loading medium and theseparation medium. The channel may be configured to contain the loadingmedium and the separation medium such that the loading medium and theseparation medium are in fluid communication with each other, asdescribed above. For example, the channel may include a contiguouspolymeric gel monolith with various regions. Each region of thecontiguous polymeric gel monolith may have different physical and/orchemical properties. The contiguous polymeric gel monolith may include afirst region having a loading medium and a second region having aseparation medium. The flow paths of each region of the polymeric gelmonolith may be configured such that a sample first contacts the loadingmedium and then contacts the separation medium. For example, the flowpaths of the loading medium and the separation medium may besubstantially aligned with the directional axis of the elongated flowpath of the microfluidic channel in the microfluidic device.

In certain embodiments, In some cases, the elongated flow path thatincludes the separation medium has a width of 1 mm or less, such as 500μm or less, including 250 μm or less, or 200 μm or less, or 150 μm orless, or 100 μm or less, or 75 μm or less, or 50 μm or less, or 40 μm orless, or 30 μm or less, or 20 μm or less, or 10 μm or less. In someinstances, the elongated flow path that includes the separation mediumhas a width of 70 μm. In some cases, the elongated flow path thatincludes the separation medium has a length ranging from 0.5 mm to 50mm, such as from 0.5 mm to 25 mm, including from 1 mm to 20 mm, or from5 mm to 15 mm. In certain embodiments, the elongated flow path thatincludes the separation medium has a length of 10 mm. In certaininstances, the elongated flow path that includes the separation mediumhas a depth of 100 μm or less, such as 75 μm or less, including 50 μm orless, or 25 μm or less, or 20 μm or less, or 15 μm or less, or 10 μm orless, or 5 μm or less. In some instances, the elongated flow path thatincludes the separation medium has a depth of 10 μm. The dimensions ofthe separation medium itself may be similar to the widths, lengths anddepths listed above.

Aspects of the microfluidic device also include embodiments that havetwo or more elongated flow paths, each of which includes a separationmedium as described above. The two or more elongated flow paths may bearranged on the microfluidic device in parallel or in series. Forinstance, the two or more elongated flow paths may be arranged inparallel, which, in some embodiments, may facilitate the analysis of twoor more samples simultaneously. Microfluidic devices may include 2 ormore, such as 4 or more, including 8 or more, 12 or more, 16 or more, 20or more, 24 or more, 36 or more, 54 or more, or 100 or more elongatedflow paths arranged in parallel. In some cases, the two or moreelongated flow paths may be arranged in series. For example, themicrofluidic device may include a first elongated flow path and a secondelongated flow path arranged in series. In some instances, arranging theelongated flow paths in series may facilitate the subsequent analysis ofconstituents in the sample that are not retained by the separationmedium in the first elongated flow path.

In certain embodiments, the microfluidic device has a width ranging from1 mm to 10 cm, such as from 5 mm to 5 cm, including from 5 mm to 1 cm.In some instances, the microfluidic device has a length ranging from 1mm to 100 cm, such as from 1 mm to 50 cm, including from 5 mm to 10 cm,or from 5 mm to 1 cm. In certain aspects, the microfluidic device has anarea of 1000 cm² or less, such as 100 cm² or less, including 50 cm² orless, for example, 10 cm² or less, or 5 cm² or less, or 3 cm² or less,or 1 cm² or less, or 0.5 cm² or less, or 0.25 cm² or less, or 0.1 cm² orless.

Further aspects related to microfluidic devices, separation media formicrofluidic devices, and methods for using microfluidic devices arefound in U.S. application Ser. No. 13/055,679, filed Jan. 24, 2011, thedisclosure of which is incorporated herein by reference in its entirety.

FIG. 1B shows a photograph of a microfluidic device according toembodiments of the present disclosure. The microfluidic device may alsoinclude various microfluidic ports, such as access ports. For example, apair of microfluidic ports may be associated with each channel, with afirst port at an upstream end of the channel and a second port at adownstream end of the channel. As shown in the photograph in FIG. 1B,the microfluidic device may include multiple parallel channels that eachcontain a separation medium. One or more channels may be in fluidcommunication with each pair of access port, such as 1 channel, 2channels, 3 channels, 4 channels, 5 channels, 6 channels, 7 channels, 8channels, 9 channels, or 10 or more channels. In the embodiment shown inFIG. 1B, each pair of access ports has four corresponding channels thateach contain a separation medium.

Methods

Embodiments of the methods are directed to separating constituents in afluid sample. In certain embodiments of the methods, one or moreconstituents in the sample may be separated. The method includesseparating a sample that includes a molecule of interest to obtain aseparation pattern. In some instances, a microfluidic device asdescribed above may be used to separate the sample, and thus the methodincludes microfluidically separating the sample that includes themolecule to obtain a separation pattern. In some instances, as describedabove, the separation medium is configured to separate the constituentsin the sample based on an equilibrium separation technique. For example,the method may include microfluidically separating the sample using anequilibrium separation technique, such as, but not limited toisoelectric focusing (IEF). In these instances, the separation patternproduced corresponds to the pattern of separated constituents in thesample after performing the equilibrium separation technique (e.g.,IEF). In other embodiments, the separation medium is configured toseparate the constituents in the sample based on a non-equilibriumseparation technique. For example, the method may includemicrofluidically separating the sample using a non-equilibriumseparation technique, such as gel electrophoresis separation techniques,including, but not limited to, PAGE, SDS-PAGE, and the like. In theseinstances, the separation pattern produced corresponds to the pattern ofseparated constituents in the sample after performing thenon-equilibrium separation technique (e.g., PAGE).

The method further includes determining a switching characteristic ofthe molecule from the separation pattern. By “switching characteristic”is meant a physicochemical property of the molecule that changes (i.e.,switches) from a first state to a second state in response to anexternal stimulus. The switching characteristic may include anydetectable physicochemical property of the molecule, such as, but notlimited to, isoelectric point, charge, electrophoretic mobility,fluorescence, binding affinity, conformation, molecular weight,hydrophobicity, and the like. In some instances, the switchingcharacteristic is the isoelectric point of the molecule of interest. Insome cases, the switching characteristic is the charge of the moleculeof interest. In some instances, the switching characteristic is aphotoswitching characteristic, such as the fluorescence of the moleculeof interest. By “photoswitching characteristic” is meant aphysicochemical property of the molecule that changes (i.e., switches)from a first state to a second state in response to an external lightstimulus. For example, the photoswitching characteristic may be a changebetween fluorescent and non-fluorescent states of the molecule. In someinstances the change between fluorescent and non-fluorescent states ofthe molecule may depend on the light the molecule is exposed, such asthe wavelength or intensity of the light the molecule is exposed to.

The external stimulus that induces the change in the switchingcharacteristic of the molecule may include, but is not limited to light,temperature, binding/cleavage events (e.g., contacting the molecule witha ligand or protease, etc.), pH of the surrounding buffer medium,contacting the molecule with a detergent or denaturant (e.g., urea), andthe like. In certain embodiments, the switching characteristic is aphotoswitching characteristic and, thus, the external stimulus thatinduces the change in the photoswitching characteristic is light. Insome instances, the photoswitching characteristic depends on thewavelength of the light. In certain cases, the photoswitchingcharacteristic may change from a first state to a second state dependingon the wavelength of the light the molecule is exposed to. For instance,the photoswitching characteristic may be in a first state upon exposureto a first wavelength of light, and may switch to a second state uponexposure to a second wavelength of light. As indicated above, thephotoswitching characteristic may be a change between fluorescent andnon-fluorescent states of the molecule. In some cases, the molecule mayswitch from a fluorescent state to a non-fluorescent state depending onthe wavelength of the light the molecule is exposed to. For instance,the molecule may be in a fluorescent state upon exposure to a firstwavelength of light, and may switch to a non-fluorescent state uponexposure to a second wavelength of light.

In certain embodiments, the method includes determining the switchingcharacteristic of the molecule. The switching characteristic may bedetermined from the separation pattern of the sample aftermicrofluidically separating the sample as described above (e.g., usingIEF or PAGE, and the like). For example, the switching characteristicmay be determined based on the isoelectric point of the molecule ofinterest, which in turn is detected using IEF as described above. Insome cases, the isoelectric point of the molecule may change from afirst state to a second state in response to an external stimulus (e.g.,an external light stimulus). For example, the isoelectric point maychange as the molecule switches from a fluorescent state to anon-fluorescent state as described above. In some instances the changebetween fluorescent and non-fluorescent states of the molecule alsoinduces a change in the isoelectric point of the molecule. The change inisoelectric point of the molecule may correspondingly be detected usingIEF. For example, a change in the separation pattern of the sample maybe detected as the isoelectric point of the molecule switches from afirst state to a second state in response to the external stimulus(e.g., external light stimulus). In some cases, the change in theseparation pattern may be detected by a shift in the corresponding IEFband of the molecule of interest (see, e.g., FIG. 24). Other switchingcharacteristics of the molecule of interest may similarly be detected asa detectable change in a corresponding physicochemical property of themolecule similar to the method described above.

In certain embodiments, the method includes determining a kineticproperty of the switching characteristic of the molecule. For instance,the method may include determining the rate of change for the switchingcharacteristic as the molecule switches from a first state to a secondstate. In some cases, the method may include determining the rate ofchange for the switching characteristic as the molecule switches fromthe second state to the first state. In some instances, the methodincludes determining the rate of photoswitching between fluorescent andnon-fluorescent states as described above, or the rate of photoswitchingbetween non-fluorescent and fluorescent states as described above. Insome cases, the method includes determining the rate of switchingbetween a first isoelectric point and a second isoelectric point asdescribed above, or the rate of switching between the second isoelectricpoint and the first isoelectric point as described above.

In certain embodiments, the method includes determining a mechanism ofthe switching characteristic of the molecule. For example, the methodmay include determining the mechanism of photoswitching betweenfluorescent and non-fluorescent states. In some cases, the mechanism maybe determined by detecting a change in a physicochemical property of themolecule as described above. For instance, the mechanism may bedetermined based on a change in the isoelectric point of the molecule inresponse to an external stimulus (e.g., an external light stimulus). Incertain instances, the mechanism of the photoswitching characteristicmay be determined from the separation pattern of the sample aftermicrofluidically separating the sample as described above (e.g., usingIEF or PAGE, and the like). For example, the mechanism of the switchingcharacteristic may be determined based on the isoelectric point of themolecule of interest, which in turn is detected using IEF as describedabove. In some cases, the isoelectric point of the molecule may changefrom a first state to a second state in response to an external stimulus(e.g., an external light stimulus). In some cases, the isoelectric pointmay change as the molecule switches from a fluorescent state to anon-fluorescent state as described above. In some instances, the changebetween fluorescent and non-fluorescent states of the molecule alsoinduces a change in the isoelectric point of the molecule. The change inisoelectric point of the molecule may correspondingly be detected usingIEF. For example, a detected increase in the isoelectric point of amolecule upon exposure to an external stimulus may indicate a switchingmechanism that includes proton uptake into the molecular structure. Viceversa, a detected decrease in the isoelectric point of the molecule mayindicate a mechanism that includes proton expulsion from the molecularstructure. A change in the separation pattern of the sample may bedetected as the isoelectric point of the molecule switches from a firststate to a second state in response to the external stimulus (e.g.,external light stimulus). In some cases, the change in the separationpattern may be detected by a shift in the corresponding IEF band of themolecule of interest (see, e.g., FIG. 24), which may facilitatedetermination of the mechanism of switching characteristic as describedabove. The mechanisms of other switching characteristics of the moleculeof interest may similarly be determined based on a detectable change ina corresponding physicochemical property of the molecule similar to themethod described above.

In certain embodiments, the method may initially include the step ofintroducing a fluid sample into a microfluidic device that includes anelongated flow path as described above. Introducing the fluid sampleinto the microfluidic device may include contacting the sample with theseparation medium, or in embodiments of the microfluidic devices thatinclude a loading medium, contacting the sample with the loading medium.The method may further include separating the sample constituents in theseparation medium to produce a separated sample, as described above. Insome cases, the separated sample is produced by gel electrophoresis asthe sample traverses the separation medium, as described above. In othercases, the separated sample is produced by isoelectric focusing in theseparation medium. The separated sample may include distinct detectablebands of constituents (e.g., analytes), where each band includes one ormore constituents that have substantially similar properties, such asmolecular mass, size, charge (e.g., charge to mass ratio), isoelectricpoint, etc. depending on the type of separation performed.

After the constituents in the sample have been separated, the method mayinclude determining the switching characteristic of the molecule asdescribed above. In other embodiments, the method includes applying astimulus to the separation medium to covalently bond the constituents tothe separation medium before detecting the molecule of interest. In somecases, the applying the stimulus includes applying electromagneticradiation to the separation medium. For instance, the method may includeexposing the separation medium to light, such as, but not limited to,visible light, UV light, infrared light, etc. In certain cases, themethod includes applying light (e.g., UV light) to the separation mediumto covalently bond the constituents to the separation medium. Furtheraspects of the separation medium, devices and methods related tocovalently bonding constituents in a sample to the separation medium aredescribed in U.S. Application Publication No. 2012/0329040, filed Jun.21, 2012, the disclosure of which is incorporated herein by reference inits entirety.

In certain embodiments, the light used to covalently bond theconstituents of interest to the separation medium has a wavelengthdifferent from the light used to activate the switching characteristicof the molecule, and different from the wavelength of light used forformation of the separation medium. For example, as described herein,the light used to activate formation of the separation medium may have awavelength of blue light in the visible spectrum. As described above,the light used to covalently bond the constituents of interest to theseparation medium may have a wavelength of UV light. As such, in certainembodiments, the method includes exposing the separation medium to afirst wavelength of light to form the separation medium, and exposingthe separation medium to a second wavelength of light to covalently bondthe constituents of interest to the separation medium. The first andsecond wavelengths of light may be blue light and UV light,respectively, as described herein.

In certain embodiments, the method includes determining whether ananalyte of interest is present in a sample, e.g., determining thepresence or absence of one or more analytes of interest in a sample. Insome instances, the microfluidic devices are configured to detect thepresence of one or more analytes in a sample. In certain embodiments ofthe methods, the presence of one or more analytes in the sample may bedetermined qualitatively or quantitatively. Qualitative determinationincludes determinations in which a simple yes/no result with respect tothe presence of an analyte in the sample is provided to a user.Quantitative determination includes both semi-quantitativedeterminations in which a rough scale result, e.g., low, medium, high,is provided to a user regarding the amount of analyte in the sample andfine scale results in which a measurement of the concentration of theanalyte is provided to the user.

In certain embodiments, the method includes detecting an analyte ofinterest bound to the separation medium. Detectable binding of ananalyte of interest to the separation medium indicates the presence ofthe analyte of interest in the sample. In some instances, detecting theanalyte of interest includes contacting the analyte of interest with alabel configured to specifically bind to the analyte of interest. Thelabel can be any molecule that specifically binds to a protein ornucleic acid sequence or biomacromolecule that is being targeted (e.g.,the analyte of interest). Depending on the nature of the analyte, thelabel can be, but is not limited to: single strands of DNA complementaryto a unique region of the target DNA or RNA sequence for the detectionof nucleic acids; antibodies against an epitope of a peptidic analytefor the detection of proteins and peptides; or any recognition molecule,such as a member of a specific binding pair. For example, suitablespecific binding pairs include, but are not limited to: a member of areceptor/ligand pair; a ligand-binding portion of a receptor; a memberof an antibody/antigen pair; an antigen-binding fragment of an antibody;a hapten; a member of a lectin/carbohydrate pair; a member of anenzyme/substrate pair; biotin/avidin; biotin/streptavidin;digoxin/antidigoxin; a member of a DNA or RNA aptamer binding pair; amember of a peptide aptamer binding pair; and the like. In certainembodiments, the label includes an antibody. The antibody mayspecifically bind to the analyte of interest.

In certain embodiments, the label includes a detectable label.Detectable labels include any convenient label that may be detectedusing the methods and systems, and may include, but are not limited to,fluorescent labels, colorimetric labels, chemiluminescent labels,multicolor reagents, enzyme-linked reagents, avidin-streptavidinassociated detection reagents, radiolabels, gold particles, magneticlabels, and the like. In certain embodiments, the label includes anantibody associated with a detectable label. For example, the label mayinclude a labeled antibody (e.g., a fluorescently labeled antibody) thatspecifically binds to the analyte of interest. As such, the method mayinclude detecting the labeled analyte of interest.

As described above, detecting the analyte of interest includescontacting the analyte of interest with a label configured tospecifically bind to the analyte of interest (e.g., an antibody thatspecifically binds to the analyte of interest). For example, detectingthe analyte of interest may include contacting the analyte of interestwith a primary label that specifically binds to the analyte of interest.In certain embodiments, the method includes enhancing the detectablesignal from the labeled analyte of interest. For instance, enhancing thedetectable signal from the labeled analyte of interest may includecontacting the primary label with a secondary label configured tospecifically bind to the primary label. In certain instances, theprimary label is a primary antibody that specifically binds to theanalyte of interest, and the secondary label is a secondary antibodythat specifically binds to the primary antibody. As such, enhancing thedetectable signal from the labeled analyte of interest may includecontacting the primary antibody with a secondary antibody configured tospecifically bind to the primary antibody. The use of two or moredetectable labels as described above may facilitate the detection of theanalyte of interest by improving the signal-to-noise ratio.

Samples that may be assayed with the subject methods may include bothsimple and complex samples. Simple samples are samples that include theanalyte of interest, and may or may not include one or more molecularentities that are not of interest, where the number of thesenon-interest molecular entities may be low, e.g., 10 or less, 5 or less,etc. Simple samples may include initial biological or other samples thathave been processed in some manner, e.g., to remove potentiallyinterfering molecular entities from the sample. By “complex sample” ismeant a sample that may or may not have the analyte of interest, butalso includes many different proteins and other molecules that are notof interest. In some instances, the complex sample assayed in thesubject methods is one that includes 10 or more, such as 20 or more,including 100 or more, e.g., 10³ or more, 10⁴ or more (such as 15,000;20,000 or 25,000 or more) distinct (i.e., different) molecular entities,that differ from each other in terms of molecular structure or physicalproperties (e.g., molecular mass, size, charge, isoelectric point,etc.).

In certain embodiments, the samples of interest are biological samples,such as, but not limited to, urine, blood, serum, plasma, saliva, semen,prostatic fluid, nipple aspirate fluid, lachrymal fluid, perspiration,feces, cheek swabs, cerebrospinal fluid, cell lysate samples, amnioticfluid, gastrointestinal fluid, biopsy tissue (e.g., samples obtainedfrom laser capture microdissection (LCM)), and the like. The sample canbe a biological sample or can be extracted from a biological samplederived from humans, animals, plants, fungi, yeast, bacteria, tissuecultures, viral cultures, or combinations thereof using conventionalmethods for the successful extraction of DNA, RNA, proteins andpeptides. In certain embodiments, the sample is a fluid sample, such asa solution of analytes in a fluid. The fluid may be an aqueous fluid,such as, but not limited to water, a buffer, and the like.

As described above, the samples that may be assayed in the subjectmethods may include one or more analytes of interest. Examples ofdetectable analytes include, but are not limited to: nucleic acids,e.g., double or single-stranded DNA, double or single-stranded RNA,DNA-RNA hybrids, DNA aptamers, RNA aptamers, etc.; proteins andpeptides, with or without modifications, e.g., antibodies, diabodies,Fab fragments, DNA or RNA binding proteins, phosphorylated proteins(phosphoproteomics), peptide aptamers, epitopes, and the like; smallmolecules such as inhibitors, activators, ligands, etc.; oligo orpolysaccharides; mixtures thereof; and the like. In certain embodiments,the molecule of interest is a protein. In some cases, the protein is afluorescent protein, such as, but not limited to, green fluorescentprotein (GFP), enhanced green fluorescent protein (EGFP), yellowfluorescent protein (YFP) and yellow fluorescent protein derivatives(e.g., Citrine, Venus, Ypet, etc.), blue fluorescent protein (BFP) andblue fluorescent protein derivatives (e.g., EBFP, EBFP2, Azurite,mKalama1, etc.), cyan fluorescent protein (CFP) and cyan fluorescentprotein derivatives (e.g., ECFP, Cerulean, CyPet, etc.), and the like.In certain instances, the fluorescent protein is GFP.

In certain embodiments, the method is configured to separate and/ordetect constituents of interest in a sample, where the sample size issmall. For example, the method may be configured to separate and/ordetect constituents of interest in a sample, where the sample size is 1mL or less, such as 750 μL or less, including 500 μL or less, or 250 μLor less, of 100 μL or less, or 75 μL or less, or 50 μL or less, or 40 μLor less, or 30 μL or less, or 20 μL or less, or 10 μL or less, or 5 μLor less, or 1 μL or less. In some instances, the method is configured toseparate and/or detect constituents of interest in a sample, where thesample size is 20 μL or less.

In certain embodiments, the method includes concentrating, diluting, orbuffer exchanging the sample prior to directing the sample through theseparation medium. Concentrating the sample may include contacting thesample with a concentration medium prior to contacting the sample withthe separation medium. The concentration medium may include a small poresize polymeric gel, a membrane (e.g., a size exclusion membrane),combinations thereof, and the like. Concentrating the sample prior tocontacting the sample with the separation medium may facilitate anincrease in the resolution between the bands of analytes in theseparated sample because each separated band of analyte may disperseless as the sample traverses through the separation medium. Diluting thesample may include contacting the sample with additional buffer prior tocontacting the sample with the separation medium. Buffer exchanging thesample may include contacting the sample with a buffer exchange mediumprior to contacting the sample with the separation medium. The bufferexchange medium may include a buffer different from the sample buffer.The buffer exchange medium may include, but is not limited to, amolecular sieve, a porous resin, and the like.

In certain embodiments, the method includes contacting the separatedanalytes bound to the separation medium with a blocking reagent prior todetecting the analyte of interest. In some cases, contacting theseparated analytes with a blocking reagent prior to detecting theanalyte of interest may facilitate a minimization in non-specificbinding of a detectable label to the separated analytes. For example,contacting the separated analytes with the blocking reagent prior todetecting the analyte of interest may facilitate a minimization innon-specific binding of a labeled antibody to the separated analytes.The blocking reagent can be any blocking reagent that functions asdescribed above, and may include, but is not limited to, bovine serumalbumin (BSA), non-fat dry milk, casein, and gelatin. In otherembodiments, no blocking step is required. Thus, in these embodiments,the method does not include a blocking step prior to detecting theanalyte of interest.

In certain embodiments, the method also includes optional washing steps,which may be performed at various times before, during and after theother steps in the method. For example, a washing step may be performedafter binding the separated sample to the separation medium, aftercontacting the separated sample with the blocking reagent, aftercontacting the separated sample with the detectable label, etc.

Embodiments of the method may also include releasing the analyte boundto the separation medium. The releasing may include contacting the boundanalyte with a releasing agent. The releasing agent may be configured todisrupt the binding interaction between the analyte and the separationmedium. In some cases, the releasing agent is a reagent, buffer, or thelike, that disrupts the binding interaction between the analyte and theseparation medium causing the separation medium to release the analyte.After releasing the analyte from the separation medium, the method mayinclude transferring the analyte away from the separation medium. Forexample, the method may include directing the released analytedownstream from the separation medium for secondary analysis with asecondary analysis device such as, but is not limited to, a UVspectrometer, and IR spectrometer, a mass spectrometer, an HPLC, anaffinity assay device, a second microfluidic device as described herein,and the like.

In some embodiments, the methods include the uniplex analysis of ananalyte in a sample. By “uniplex analysis” is meant that a sample isanalyzed to detect the presence of one analyte in the sample. Forexample, a sample may include a mixture of an analyte of interest andother molecular entities that are not of interest. In some cases, themethods include the uniplex analysis of the sample to determine thepresence of the analyte of interest in the sample mixture.

Certain embodiments include the multiplex analysis of two or moreanalytes in a sample. By “multiplex analysis” is meant that the presencetwo or more distinct analytes, in which the two or more analytes aredifferent from each other, is determined. For example, analytes mayinclude detectable differences in their molecular mass, size, charge(e.g., mass to charge ratio), isoelectric point, and the like. In someinstances, the number of analytes is greater than 2, such as 4 or more,6 or more, 8 or more, etc., up to 20 or more, e.g., 50 or more,including 100 or more, distinct analytes. In certain embodiments, themethods include the multiplex analysis of 2 to 100 distinct analytes,such as 4 to 50 distinct analytes, including 4 to 20 distinct analytes.In certain embodiments, multiplex analysis also includes the use of twoor more different detectable labels. The two or more differentdetectable labels may specifically bind to the same or differentanalytes. In some cases, the two or more different detectable labels mayspecifically bind to the same analyte. For instance, the two or moredifferent detectable labels may include different antibodies specificfor different epitopes on the same analyte. The use of two or moredetectable labels specific for the same analyte may facilitate thedetection of the analyte by improving the signal-to-noise ratio. Inother cases, the two or more different detectable labels mayspecifically bind to different analytes. For example, the two or moredetectable labels may include different antibodies specific for epitopeson different analytes. The use of two or more detectable labels eachspecific for different analytes may facilitate the detection of two ormore respective analytes in the sample in a single assay.

In certain embodiments, the method is an automated method. As such, themethod may include a minimum of user interaction with the microfluidicdevices and systems after introducing the sample into the microfluidicdevice. For example, the steps of separating the sample constituents inthe separation medium to produce a separated sample and applying thestimulus to the separation medium to covalently bond the constituents tothe separation medium may be performed by the microfluidic device andsystem, such that the user need not manually perform these steps. Insome cases, the automated method may facilitate a reduction in the totalassay time. For example, embodiments of the method, including theseparation and detection of analytes in a sample, may be performed in120 minutes or less, such as 90 minutes or less, or 60 minutes or less,or 45 minutes or less, or 30 minutes or less, such as 20 minutes orless, including 15 minutes or less, or 10 minutes or less, or 5 minutesor less, or 2 minutes or less, or 1 minute or less.

FIG. 1A shows a workflow illustration of an embodiment of a method forseparating constituents of a fluid sample. In the embodiment shown inFIG. 1A, the method includes isoelectric focusing (IEF) of the sampleconstituents followed by post-separation binding to the separationmedium and, finally, detection using a labeled antibody probe. Analytesare identified in situ by specific affinity interactions. In step (i) ofFIG. 1A, a sample is contacted with the separation medium. After thesample is contacted with the separation medium, an electric field isapplied along the directional axis of the separation medium to focusconstituents in the sample based in the isoelectric point (pI) of theconstituents. In step (ii) of FIG. 1A, the various analytes in thesample constituents have been separated by IEF in the separation medium,and the separation medium is exposed to UV light to covalently bond theconstituents to the separation medium. In step (iii) of FIG. 1A, theseparation medium is washed, for example to wash out the pH gradientused for IEF from the separation medium. In step (iv) of FIG. 1A, adetectable label (e.g., a fluorescently labeled antibody) is contactedwith the separated analytes bound to the separation medium. Thedetectable label specifically binds to the analyte of interest (e.g.,the target protein). Unbound label is washed away to facilitate areduction in background signal (step (v) of FIG. 1A). A positivedetection of the detectable label indicates the presence of the analyteof interest in the sample.

Aspects of embodiments of the methods may also include methods ofproducing a separation medium in a flow path. The method of producingthe separation medium in the flow path may include providing precursormoieties in the flow path. For instance, the flow path may be filledwith the precursor moieties (e.g., gel precursors, such aspolyacrylamide gel precursors). In some cases, the method includesactivating the precursor moieties to form the separation medium. Forexample, activating the gel precursors may include chemically activatingthe gel precursors by contacting the gel precursors with an activationagent, such as, but not limited to, a peroxide. In certain cases,activating the gel precursors includes photo-activating the gelprecursors by contacting the gel precursors with light. As describedabove, the light used to activate formation of the separation medium mayhave a wavelength of blue light in the visible spectrum. For instance,the light used to activate formation of the separation medium may have awavelength ranging from 400 nm to 500 nm, such as from 410 nm to 490 nm,including from 420 nm to 480 nm, or from 430 nm to 480 nm, or from 440nm to 480 nm, or from 450 nm to 480 nm, or from 460 nm to 480 nm, orfrom 465 nm to 475 nm. In certain cases, the light used to activateformation of the separation medium has a wavelength ranging from 465 to475 nm. In some instances, the light used to activate formation of theseparation medium has a wavelength of 470 nm.

Systems

Aspects of certain embodiments include a system for separatingconstituents in a fluid sample. In some instances, the system includes amicrofluidic device as described herein. The system may also include asource of electromagnetic radiation (i.e., an electromagnetic radiationsource). In certain embodiments, the system includes a module configuredto perform a method of assaying molecule switching as described in moredetail below. For example, the module may be configured to determine aswitching characteristic of a molecule from a switching pattern producedby microfluidically separating a sample that includes the molecule usinga microfluidic device as described herein.

In certain embodiments, the module includes a processor. The processormay be configured to execute programming that includes instructions forcontrolling the system to perform one or more of the steps in the methoddescribed herein. For instance, the processor may be configured toexecute programming that includes instructions for determining aswitching characteristic of a molecule from a switching pattern producedby microfluidically separating a sample that includes the molecule usinga microfluidic device as described herein.

In certain embodiments, the electromagnetic radiation source is a lightsource. For example, the light source may include a visible lightsource, a UV light source, an infrared light source, etc. In someinstances, the electromagnetic radiation source includes a light source,such as a UV light source. As described above, the electromagneticradiation source may be used to apply electromagnetic radiation to theseparation medium in the microfluidic device to covalently bond sampleconstituents to the separation medium.

In certain embodiments, the system also includes a detector. In somecases, the detector is a detector configured to detect a detectablelabel. The detector may include any type of detector configured todetect the detectable label used in the assay. As described above,detectable label may be a fluorescent label, colorimetric label,chemiluminescent label, multicolor reagent, enzyme-linked reagent,avidin-streptavidin associated detection reagent, radiolabel, goldparticle, magnetic label, etc. In some instances, the detectable labelis a fluorescent label. In these instances, the detector may beconfigured to contact the fluorescent label with electromagneticradiation (e.g., visible, UV, X-ray, etc.), which excites thefluorescent label and causes the fluorescent label to emit detectableelectromagnetic radiation (e.g., visible light, etc.). The emittedelectromagnetic radiation may be detected by the detector to determinethe presence of the labeled analyte bound to the separation medium.

In some instances, the detector may be configured to detect emissionsfrom a fluorescent label, as described above. In certain cases, thedetector includes a photomultiplier tube (PMT), a charge-coupled device(CCD), an intensified charge-coupled device (ICCD), a complementarymetal-oxide-semiconductor (CMOS) sensor, a visual colorimetric readout,a photodiode, and the like.

Systems of the present disclosure may include various other componentsas desired. For example, the systems may include fluid handlingcomponents, such as microfluidic fluid handling components. The fluidhandling components may be configured to direct one or more fluidsthrough the microfluidic device. In some instances, the fluid handlingcomponents are configured to direct fluids, such as, but not limited to,fluid samples, buffers (e.g., electrophoresis buffers, wash buffers,release buffers, etc.), and the like. In certain embodiments, themicrofluidic fluid handling components are configured to deliver a fluidto the separation medium of the microfluidic device, such that the fluidcontacts the separation medium. The fluid handling components mayinclude microfluidic pumps. In some cases, the microfluidic pumps areconfigured for pressure-driven microfluidic handling and routing offluids through the microfluidic devices and systems disclosed herein. Incertain instances, the microfluidic fluid handling components areconfigured to deliver small volumes of fluid, such as 1 mL or less, suchas 500 μL or less, including 100 μL or less, for example 50 μL or less,or 25 μL or less, or 10 μL or less, or 5 μL or less, or 1 μL or less.

In certain embodiments, the systems include one or more electric fieldgenerators. An electric field generator may be configured to apply anelectric field to various regions of the microfluidic device. The systemmay be configured to apply an electric field such that the sample iselectrokinetically transported through the microfluidic device. Forexample, the electric field generator may be configured to apply anelectric field to the separation medium. In some cases, the appliedelectric field may be aligned with the directional axis of theseparation medium. As such, the applied electric field may be configuredto electrokinetically transport the analytes and components in a samplethrough the separation medium. In some instances, the electric fieldgenerators are configured to apply an electric field with a strengthranging from 10 V/cm to 1000 V/cm, such as from 100 V/cm to 800 V/cm,including from 200 V/cm to 800 V/cm, or from 400 v/cm to 800 V/cm.

In certain embodiments, the system includes an electric field generatorconfigured to apply an electric field such that analytes and/orconstituents in the sample are isoelectrically focused in the separationmedium. For instance, an applied electric field may be aligned with thedirectional axis of the separation medium and configured toisoelectrically focus the sample constituents along the directional axisof the separation medium.

In certain embodiments, the subject system is a biochip (e.g., abiosensor chip). By “biochip” or “biosensor chip” is meant amicrofluidic system that includes a substrate surface which displays twoor more distinct microfluidic devices on the substrate surface. Incertain embodiments, the microfluidic system includes a substratesurface with an array of microfluidic devices.

An “array” includes any two-dimensional or substantially two-dimensional(as well as a three-dimensional) arrangement of addressable regions,e.g., spatially addressable regions. An array is “addressable” when ithas multiple devices positioned at particular predetermined locations(e.g., “addresses”) on the array. Array features (e.g., devices) may beseparated by intervening spaces. Any given substrate may carry one, two,four or more arrays disposed on a front surface of the substrate.Depending upon the use, any or all of the arrays may be the same ordifferent from one another and each may contain multiple distinctmicrofluidic devices. An array may contain one or more, including two ormore, four or more, eight or more, 10 or more, 25 or more, 50 or more,or 100 or more microfluidic devices. In certain embodiments, themicrofluidic devices can be arranged into an array with an area of 100cm² or less, 50 cm² or less, or 25 cm² or less, 10 cm² or less, 5 cm² orless, such as 1 cm² or less, including 50 mm² or less, 20 mm² or less,such as 10 mm² or less, or even smaller. For example, microfluidicdevices may have dimensions in the range of 10 mm×10 mm to 200 mm×200mm, including dimensions of 100 mm×100 mm or less, such as 50 mm×50 mmor less, for instance 25 mm×25 mm or less, or 10 mm×10 mm or less, or 5mm×5 mm or less, for instance, 1 mm×1 mm or less.

Arrays of microfluidic devices may be arranged for the multiplexanalysis of samples. For example, multiple microfluidic devices may bearranged in series, such that a sample may be analyzed for the presenceof several different analytes in a series of microfluidic devices. Incertain embodiments, multiple microfluidic devices may be arranged inparallel, such that two or more samples may be analyzed at substantiallythe same time.

Aspects of the systems include that the microfluidic devices may beconfigured to consume a minimum amount of sample while still producingdetectable results. For example, the system may be configured to use asample volume of 100 μL or less, such as 75 μL or less, including 50 μLor less, or 25 μL or less, or 10 μL or less, for example, 5 μL or less,2 μL or less, or 1 μL or less while still producing detectable results.In certain embodiments, the system is configured to have a detectionsensitivity of 1 nM or less, such as 500 pM or less, including 100 pM orless, for instance, 1 pM or less, or 500 fM or less, or 250 fM or less,such as 100 fM or less, including 50 fM or less, or 25 fM or less, or 10fM or less. In some instances, the system is configured to be able todetect analytes at a concentration of 1 μg/mL or less, such as 500 ng/mLor less, including 100 ng/mL or less, for example, 10 ng/mL or less, or5 ng/mL or less, such as 1 ng/mL or less, or 0.1 ng/mL or less, or 0.01ng/mL or less, including 1 pg/mL or less. In certain embodiments, thesystem has a dynamic range from 10⁻¹⁸ M to 10 M, such as from 10⁻¹⁵ M to10⁻³ M, including from 10⁻¹² M to 10⁻⁶ M.

In some cases, the system is configured to have a signal-to-noise ratio(SNR) of 10 or more, such as 15 or more, including 20 or more, or 30 ormore, or 40 or more, or 50 or more, or 60 or more, or 70 or more, or 80or more, or 90 or more, or 100 or more, or 150 or more, or 200 or more,or 500 or more, or 1,000 or more, or 2,000 or more, or 3,000 or more, or4,000 or more, or 5,000 or more, or 6,000 or more, or 7,000 or more, or8,000 or more, or 9,000 or more, or 10,000 or more. In some cases, theachievable signal-to-noise ratio depends on the method of detection usedin the assay. For example, in certain embodiments the analyte ofinterest is directly labeled with a detectable label. In theseembodiments, the signal-to-noise ratio may be 10 or more, such as 15 ormore, including 20 or more, or 30 or more, or 40 or more, or 50 or more,or 60 or more, or 70 or more, or 80 or more, or 90 or more, or 100 ormore, or 150 or more, or 200 or more. In other embodiments, the analyteof interest is first labeled with a primary label (e.g., a primaryantibody) and then the primary label is labeled with a secondary label(e.g., a secondary antibody). In these embodiments, the signal-to-noiseratio may be 100 or more, such as 150 or more, including 200 or more, or500 or more, or 1,000 or more, or 2,000 or more, or 3,000 or more, or4,000 or more, or 5,000 or more, or 6,000 or more, or 7,000 or more, or8,000 or more, or 9,000 or more, or 10,000 or more.

In certain embodiments, the microfluidic devices are operated at atemperature ranging from 1° C. to 100° C., such as from 5° C. to 75° C.,including from 10° C. to 50° C., or from 20° C. to 40° C. In someinstances, the microfluidic devices are operated at a temperatureranging from 35° C. to 40° C.

Utility

The subject devices, systems and methods find use in a variety ofdifferent applications where the determination of characteristicsrelated to molecule switching is desired. For example, the dynamic andprobed IEF assays described herein find use in analytical screening andquantitative kinetic analysis of photoswitching and other chargeswitching processes in response to stimuli including light, temperature,binding/cleavage events (e.g., contacting the molecule with a ligand orprotease, etc.), pH of the surrounding buffer medium, contacting themolecule with a detergent or denaturant (e.g., urea), and the like. Thesubject devices, systems and methods also find use in other equilibriumand non-equilibrium separations and other switching processes where adifferent property is altered from switching (e.g., electrophoreticmobility altered due to ligand binding/unbinding during polyacrylamidegel electrophoresis (PAGE)).

The subject devices, systems and methods also find use in themeasurement of dynamic protein reaction processes in real time. Forexample, the subject devices, systems and methods may be used todetermine dynamic protein processes, including the photophysics offluorescent proteins. Dynamic IEF analysis as described herein may beused to resolve and track fluorescent protein populations throughphysicochemical properties rather than by traditional fluorescence orstatic crystallographic measurements. As such, the subject devices,systems and methods find use in probing the chemical and structuralnature of conformational photoswitching processes. The subject devices,systems and methods find use in the analysis of a range of fluorescentand other light-reactive proteins. For example, the ability tocharacterize GFP constructs genetically encoded with light-switchablecharge may be used for a broad range of applications, such as the studyof cellular membrane transport processes and the rational engineering ofelectrostatic aggregation in signaling molecule or metabolic networks.The subject devices, systems and methods find use in the study ofreversible fluorescence (and thus isoelectric point) photoswitching atpH values in the vicinity of the fluorescence pK_(a)s of GFPs, whichindicates that mutants developed as sensitive pH indicators in thephysiologic range may be used for achieving maximum charge switching inbiological systems. Other photoactivatable GFPs (e.g., Dronpa, Padron0.9and PA-GFP, and the like) may also find use as described above.

Charge-switchable proteins may also find use in the engineering ofbiomimetic smart materials with light-actuated transitions in zetapotential, hydrophilicity/wetting behavior, and adhesion properties. Thesubject devices, systems and methods for dynamic IEF also find use inhigh-throughput screening for rational or directed tuning ofphotoactivatable protein phenomena, such as reversible photochromism andlight-induced protein-protein interactions. The subject devices, systemsand methods for dynamic and probed IEF assays also find use inanalytical screening and quantitative kinetic analysis of photoswitchingand other charge switching processes in response to stimuli includinglight, temperature, or binding/cleavage events.

The subject devices, systems and methods described herein can also beused with other equilibrium separations such temperature gradientfocusing (TGF), isotachophoresis (ITP), and non-equilibrium separationtechniques such as PAGE, chromatography, etc. In addition tophotoswitching, the switching mechanism can be any other that altersphysicochemical properties screened in the separation (examples includecleavage, ligand association/dissociation, etc.). The property alteredcan be different than pI, for example charge, molecular weight,conformation, electrophoretic mobility, hydrophobicity, etc. Theswitching can also be modulated by other external stimuli such astemperature, introduction of ligand, proteases, detergent, urea, etc.The switching could also occur spontaneously, such as a protein adoptingdifferent conformation states during electromigration.

Analyte probing and visualization can be done with reagents other thanantibodies such as affibodies, aptamers, dyes, enzyme conjugates, etc.Readout methods other than fluorescence such as contactless conductance,absorbance, etc. can be used to determine band morphology duringseparation or after immobilization.

The subject devices, systems and methods find use in the determinationof the presence or absence, and/or quantification of one or moreanalytes in a sample. For example, the subject devices, systems andmethods find use in the separation and detection of proteins, peptides,nucleic acids, and the like. In some cases, the subject devices, systemsand methods find use in the separation and detection of proteins.

In some instances, the subject devices, systems and methods can be usedwithout requiring a laboratory setting for implementation. In comparisonto the equivalent analytic research laboratory equipment, the subjectdevices and systems provide comparable analytic sensitivity in aportable, hand-held system. In some cases, the mass and operating costare less than the typical stationary laboratory equipment. The subjectsystems and devices may be integrated into a single apparatus, such thatall the steps of the assay, including separation, transfer, labeling anddetecting of an analyte of interest, may be performed by a singleapparatus. For example, in some instances, there are no separateapparatuses for separation, transfer, labeling and detecting of ananalyte of interest. In addition, the subject systems and devices can beutilized in a home setting for over-the-counter home testing by a personwithout medical training to detect one or more analytes in samples. Thesubject systems and devices may also be utilized in a clinical setting,e.g., at the bedside, for rapid diagnosis or in a setting wherestationary research laboratory equipment is not provided due to cost orother reasons.

Kits

Aspects of the present disclosure additionally include kits that have amicrofluidic device as described in detail herein. The kits may furtherinclude a buffer. For instance, the kit may include a buffer, such as anelectrophoresis buffer, a sample buffer, and the like. In certain cases,the buffer is an electrophoresis buffer, such as, but not limited to, aTris buffer, a Tris-glycine, and the like. In some instances, the bufferincludes a detergent (such as sodium dodecyl sulfate, SDS).

The kits may further include additional reagents, such as but notlimited to, release reagents, denaturing reagents, refolding reagents,detergents, detectable labels (e.g., fluorescent labels, colorimetriclabels, chemiluminescent labels, multicolor reagents, enzyme-linkedreagents, detection reagents (e.g., avidin-streptavidin associateddetection reagents), calibration standards, radiolabels, gold particles,magnetic labels, etc.), and the like.

In certain embodiments, the kits include a detectable label. Thedetectable label may be associated with a member of a specific bindingpair. Suitable specific binding pairs include, but are not limited to: amember of a receptor/ligand pair; a ligand-binding portion of areceptor; a member of an antibody/antigen pair; an antigen-bindingfragment of an antibody; a hapten; a member of a lectin/carbohydratepair; a member of an enzyme/substrate pair; biotin/avidin;biotin/streptavidin; digoxin/antidigoxin; a member of a DNA or RNAaptamer binding pair; a member of a peptide aptamer binding pair; andthe like. In certain embodiments, the member of the specific bindingpair includes an antibody. The antibody may specifically bind to ananalyte of interest in the separated sample bound to the separationmedium. For example, the detectable label may include a labeled antibody(e.g., a fluorescently labeled antibody) that specifically binds to theanalyte of interest.

In addition to the above components, the subject kits may furtherinclude instructions for practicing the subject methods. Theseinstructions may be present in the subject kits in a variety of forms,one or more of which may be present in the kit. One form in which theseinstructions may be present is as printed information on a suitablemedium or substrate, e.g., a piece or pieces of paper on which theinformation is printed, in the packaging of the kit, in a packageinsert, etc. Another means would be a computer readable medium, e.g.,diskette, CD, DVD, Blu-Ray, computer-readable memory, etc., on which theinformation has been recorded or stored. Yet another means that may bepresent is a website address which may be used via the Internet toaccess the information at a removed site. Any convenient means may bepresent in the kits.

As can be appreciated from the disclosure provided above, embodiments ofthe present invention have a wide variety of applications. Accordingly,the examples presented herein are offered for illustration purposes andare not intended to be construed as a limitation on the invention in anyway. Those of ordinary skill in the art will readily recognize a varietyof noncritical parameters that could be changed or modified to yieldessentially similar results. Thus, the following examples are put forthso as to provide those of ordinary skill in the art with a completedisclosure and description of how to make and use the present invention,and are not intended to limit the scope of what the inventors regard astheir invention nor are they intended to represent that the experimentsbelow are all or the only experiments performed. Efforts have been madeto ensure accuracy with respect to numbers used (e.g. amounts,temperature, etc.) but some experimental errors and deviations should beaccounted for. Unless indicated otherwise, parts are parts by mass,molecular mass is mass average molecular mass, temperature is in degreesCelsius, and pressure is at or near atmospheric.

EXAMPLES Example 1

1. Multi-Stage, Single-Channel Assay Under Programmable ElectrophoreticControl

The microfluidic device included a single microchannel housing aphotoactive polyacrylamide gel matrix to integrate three assay stages(FIG. 1A): Separation—(i) sample loading and isoelectric focusing;Photocapture—(ii) UV exposure to covalently attach IEF-resolved proteinisoforms to the separation medium followed by (iii) electrophoreticmobilization and washout of uncaptured species; and Probing—(iv)electrophoretic-introduction of antibody to the immobilized proteinbands and (v) electrophoretic washout of unbound detection antibodies.Two or more microfluidic devices can be run in parallel on a singlemicrofluidic chip (FIG. 1B).

In the first stage of the assay, proteinaceous samples were prepared andloaded in an ampholyte buffer titrated to the alkaline limit of thebuffering range (˜pH 10 for Pharmalyte 3-10) to minimize electrophoreticloading bias. After addition of anolyte and catholyte to the terminalreservoirs, an electric field was applied and IEF focused the analytesat channel positions determined by the pI of the analyte relative to theaxial pH gradient. Recombinant wtGFP was included in the unlabeledprotein mixture as a loading and immobilization standard along with amixture of fluorescent pI marker peptides that absorb in the UV. Steppedramping of the applied electric field (50 to 300 V cm⁻¹ in 50-100 V cm⁻¹increments) yielded focusing of analytes in <20 min (FIGS. 1C and 1D).Analysis of the pI marker peptides indicated that repeatable, linear pHgradients were achieved (y=10.8−7.53x, where x is the fractional channeldistance from the cathode; within-chip % RSD in slope of 6.5%, n=16,R²>0.99 for all fits over pH 4-8.7 range).

The second stage of the assay was a transition between the IEF andimmunoprobing stage, with the immunoprobing taking place in situ (i.e.,no transfer of sample to a blotting membrane). The separation mediumcontaining the focused analytes was exposed to UV light (350-365 nm, 10sec), which induced photoimmobilization of analytes by thelight-activatable copolymer gel matrix. Exposure to UV promoted thecarbonyl groups of the benzophenone methacrylamide (BPMA) monomertermini to an electrophilic triplet state, T₁*. Subsequent hydrogenabstraction was preferential towards C—H bonds in target polypeptides({circle around (P)}) and other buffer constituents, leading toformation of stable covalent linkages to the gel matrix (see FIG. 6 andFIG. 7).

After UV exposure, uniform pH buffer conditions were recovered bychemical mobilization and washout of the pH gradient from the channel.Chemical mobilization was initiated by applying glycine buffer (pH 9.9)and an electric field at the access wells, resulting in elution ofuncaptured species into the anodic well within 20 min (FIG. 1E).

In the third assay stage, the re-established homogeneous bufferconditions permitted electrophoretic introduction of immunoaffinityprobes (fluorescently labeled detection antibodies, pAb*=polyclonalantibody, mAb*=monoclonal antibody) into the protein-decorated gel (FIG.1F). Electromigration of the probes through the nanoporous gel matrixfacilitated efficient mass transfer of probe to captured targetanalytes. A final 20 min electrophoretic washout of free probe resultedin the target protein isoform pattern (FIG. 2A). Additional secondaryantibody probing can be employed to improve assay sensitivity. Specificdetection of wtGFP isoforms yielded a pAb* red fluorescence readout thatreplicated the native green fluorescence readout of the captured wtGFPagainst a ˜20-fold excess of off-target ladder proteins. Analysis ofwtGFP indicated a minimum resolvable pI difference of 0.15 pH units anda peak capacity of 110±22 (n=3 isoforms) (FIG. 8).

2. Isoelectric Photoswitching of wtGFP

Directly comparing the focused, captured and probed isoform patterns ofwtGFP enabled identification of an isoform with reversiblyphotoswitchable fluorescence and pI. When wtGFP was briefly exposed toblue light (460-500 nm, 120 sec, in the focused state), the wtGFPisoform profile exhibited three canonical isoforms with pI's of 4.88,5.00 and 5.19 (see FIG. 2A). When wtGFP was not exposed to blue light, afourth isoform (pI˜5.33) complemented the three expected wtGFP isoforms.The pI 5.33 peak accounted for ˜16% of the GFP mass.

A dynamic photoswitching process was observable in real time using anIEF separation medium. Exposure of focused “dark-state” wtGFP to bluelight switched on the fluorescence of the pI 5.33 peak. IEF monitoringallowed estimation of the “on” time constant at 420 msec (FIG. 2B).Further, dynamic “retreat” of the pI 5.33 wtGFP isoform towards thedominant peak (pI 5.00) was observed on the 5-10 sec timescale (FIG.2B). This light-activated migration process was partially reversibleunder subsequent dark-light cycles. Without being limited to anyparticular theory, the pI switching behavior may be due to chromophorephotoconversion and charge transfer phenomena. For example, thephotoswitching peak may be the protonated (neutral) chromophorepopulation, with blue light excitation leading to chromophoredeprotonation and proton transfer to the solvent along an internal“proton wire”. The reversible decrease in pI of this isoform indicatessolvent accessibility of the labile wtGFP chromophore proton.

3. Capture Kinetics Inform Photoimmobilization Conditions

Experiments were performed to identify conditions for optimal mapping ofthe IEF separation to the separation medium during photoimmobilization.IEF exhibited cathodic drift due to the slight negative charge ofpolyacrylamide gels and the associated EOF. The separation mediumcathodic drift velocity u_(drift) was 1.0 μm s⁻¹<u_(drift)<3.3 μm s⁻¹(E_(IEF)=300 V cm⁻¹ at IEF completion). Thus, a 10 s UV exposure(Δt_(UV)) during photoimmobilization yielded a drift distance(L_(drift)=u_(drift)·Δt_(UV)) of 10-33 μm for a focused protein band.The average peak width of focused GFP isoforms (w_(ave)=4σ_(ave)) was100 μm, making L_(drift) comparable to w_(ave). As such, the UV exposuremay be performed under zero-field conditions (E=0 V cm⁻¹) to minimizecaptured analyte dispersion arising from cathodic drift.

In certain embodiments, the focusing force of IEF goes to zero underzero-field conditions with the initially focused protein bandsbroadening due to molecular diffusion. In some instances, this leads toa tradeoff between the extent of diffusional band broadening duringcapture and the duration of the photoimmobilization reaction. Thetimescale of diffusional band broadening was characterized after IEFfocusing of wtGFP. Focused GFP was allowed to “defocus” under zero-fieldconditions with real-time single-point imaging (FIG. 3A). The separationresolution, R_(s), of the pI 5.00 and 5.19 wtGFP isoform peak pairdecreased from 2.8 to 1.0 over the course of 100 s

$\left( {{R_{s} = \frac{x_{1} - x_{2}}{4\;\sigma_{ave}}},} \right.$where x₁-x₂ is the distance between peaks). The defocusing behavior wasin close agreement with the behavior expected under Fickian diffusion ofGaussian peaks.

To characterize the photoimmobilization reaction (FIG. 3B), an analyte“capture efficiency” was observed. The capture efficiency, η, wasdefined as the ratio of fluorescence measured after gradient washout(AFU_(w)) to the fluorescence during focusing (AFU_(f)), corrected by afactor ε to account for the anticipated influence of pH on the speciesfluorescence signal. In some instances, the washout buffer (pH_(w)=9.9)and the local pH of the buffer in the focused state (pH_(f)˜pI) aredifferent. Thus, the capture efficiency was:

$\begin{matrix}{\eta = {\frac{{AFU}_{w,{pHw}}}{{AFU}_{f,{pHf}}} \times ɛ_{{pHw},{pHf}} \times 100\%}} & \lbrack 1\rbrack\end{matrix}$Where the pH dependence of the fluorescence signal was measured viafree-solution microplate experiments to be: ε_(pHw=9.9,pHf≈5)≈0.75 forwtGFP and ε_(pHw=9.9,pHf=4.3-9.4)≈1 for all CE540-labeled species inthis example. The capture efficiency of wtGFP was evaluated undernon-focusing conditions using GFP uniformly distributed throughout theseparation medium. The wtGFP was then immobilized by spot UV exposurevia a 10× microscope objective (FIG. 3B). GFP photoimmobilization wasadequately described by a first order process relating η to the UVexposure time through an integrated rate law of the form

$\eta = {{a\left( {b - e^{- \frac{t}{\tau}}} \right)}.}$By least-squares fitting, the time constant τ for the immobilizationreaction was determined to be 5.5 sec (a=1.59, b=1.12). The maximumwtGFP capture efficiency was 1.8%. This capture efficiency was a morethan 100-fold improvement over the ˜0.01% reported for surfacephotoimmobilization. The significant increase in capture efficiency maybe due to the greater reactive surface area of the separation mediumaccording to embodiments of the present disclosure.

Balancing the photoimmobilization kinetics with resolution loss bydefocusing suggested an optimal exposure time of 10 sec. A Δt_(UV) of 10sec conferred 84% of the achievable capture efficiency for a decrease inseparation resolution of 22% from that in the focused-state.

4. Separation Medium Capture Efficiency has a Weak pH Dependence

Experiments were performed to verify pH-consistent photoimmobilizationperformance by determining η over a wide pH range under IEF conditions.To achieve this, the immobilization behavior of fluorescently labeledampholytes with pls in the 5-7.5 range was characterized (FIGS. 3C and3D). Ampholytes are mixtures of polyprotic amino carboxylic acids thatbuffer at their pls. The pH 5-7.5 range encompassed most protein pls(˜65% of a diverse set of 500 protein isoforms studied using macro-IEF).The red fluorescent pyrilium salt CE540 (Chromeo P540, Pye 6) wasconjugated to the amine termini of the ampholytes. A charge-compensatingreaction mechanism allowed CE540 labeling to avoid introduction ofcharge heterogeneity. The resulting red fluorescent ampholyte species(ampholyte*) were a structural analog to polypeptides, and allowed η tobe measured across a broad pH range.

FIG. 3C shows a ˜2-fold monotonic rise in the ampholyte* η between pH 5and 7.5. The η for the negative control gel (BPMA−) over this range isindistinguishable from background. Similarly, while the BPMA+signal-to-noise ratio (SNR) spanned ˜20-100 over pH 5-7.5, the BPMA− gelyielded substantially lower SNR. For further comparison, FIG. 3D showsfluorescence micrographs of ampholyte* intensity along the separationchannel for both BPMA+ and BPMA− gels after electrophoretic washout.Without being limited to any particular theory, the increase in η withpH may be due to a change in the chemical properties of the ampholytespecies, which were also graded along the pH axis. The pH response of ηwas acceptable given the absence of a strong bias towards any particularpH zone and the fact that protein isoforms were generally clustered overa relatively tight pI range. Thus, in certain embodiments, a singlecapture efficiency for all isoforms of a given target was likely to bevalid in most applications. Also plotted on FIG. 3C is η for both nativeGFP* and PSA* (10.1±1.91%, n=8; and 9.92±0.86%, n=3 respectively). Bothspecies exhibited η on par with ampholyte* capture.

Arrows in FIG. 3C indicate regions in which co-localization of pImarkers and ampholyte* produced higher ampholyte* photobleaching duringUV exposure in both BPMA+ and BPMA− gels (see FIG. 9). This exaggeratedlocal bleaching manifested as artifactual peaks in the ampholyte* ηdata.

5. Influence of Target Protein Hydrophobicity on Separation MediumCapture Efficiency

In certain embodiments, CE540 labeling effected the conformationalheterogeneity and capture efficiency of wtGFP. In some instances, theampholyte*, PSA* and native GFP* η values (at ˜10% each) were allsignificantly higher than the η of 1.30±0.17% (n=44) measured forunlabeled GFP in the focused state across several chips and experimentdays. Without being limited to any particular theory, the hydrophobicstructure of CE540 may be the source of this higher η by increasing weak“pre-covalent” interactions of labeled species with the gel matrix.

6. Assays for PSA Isoform Quantitation

Purified underivatized PSA was probed after IEF and photoimmobilizationusing sequential introduction of specific primary and secondarydetection antibodies (FIG. 4A). Two major isoforms with pls of 6.27±0.02and 6.77±0.04 (n=4) were apparent, accompanied by several minor peaksbelow baseline resolution. Macroscale slab gel IEF of PSA gave a similarisoform pattern. The PSA calibration curve is shown in FIG. 4B. In FIG.4B, the relationship between the nominal PSA concentration andfluorescence readout over the dominant isoform (pH 6.0-6.5) was linearin the range of ˜10-500 nM. Quantitative capacity was maintained to ˜5nM PSA (165 ng ml⁻¹) or ˜1.1 pg of PSA.

Based on these antibody probing analyses, the stoichiometry ofsecondary:primary Ab* binding can be inferred from the ratio of therespective fluorescence traces (FIG. 4C). In these experiments, thedegrees of labeling of each antibody probe were similar, and thelabeling dye was the same (red Alexa Fluor 568). The bindingstoichiometry was determined to be ˜2.5 across the relevant pH range,exhibiting somewhat higher values at the acidic end of the isoformpattern due to a non-specific contribution of the secondary Ab* to theassay readout.

Experiments were performed to quantify endogenous PSA isoforms presentin minimally processed cell lysate from LAPC4 human prostate cancercells (FIG. 4D). The LAPC4 cell lysate expressed PSA at a concentrationof 19.5±2.7 nM, as quantified by ELISA (n=8). As a negative control, aDU145 (PSA−) lysate was also assayed. The probed LAPC4 lysate presenteda distinctive 3-peak pattern in the pI 6.75-8 range, with non-specificsignal apparent near the anodic well (the electrophoretic introductionpoint for both sample and pAb*). This pattern was similar to thosepresented in slab gel assays of PSA purified from LNCaP cell culturemedium. The total LAPC4 PSA concentration for this assay was determinedto be 27.8±4.7 nM (n=4) from the purified PSA calibration curve of FIG.4B.

7. Assays in Isoform “Recognition Mapping” Mode

To validate the capability of assays of the present disclosure tomeasure immunoreagent isoform specificity, the isoform distribution ofIEF-focused CE540-labeled PSA* were compared to its probe fluorescencereadout after photoimmobilization and probing with mAb* and pAb* (FIG.5). Alignment between each pair of fluorescence intensity profiles(PSA*, Ab*) was accomplished by applying a translation inferred fromtheir cross-correlation. The translational shift corrected for theslight drift (˜190 μm) between imaging of focused PSA* and thephotoimmobilization step. The focused PSA* isoform pattern agreed wellwith that of the probed unlabeled PSA, suggesting minimal impact ofCE540 on the pls of the native PSA isoforms (compare FIGS. 5A and 5B toFIG. 4A). Ratiometric comparison of the probed and focused PSA* signalssuggested spatially uniform probe layering onto immobilized PSA* acrossthe pH region of interest, for both polyclonal and monoclonal detectionantibodies (FIGS. 5C and 5D). Some variation across the pH range wasinduced by diffusional band broadening during photoimmobilization, whichhad the expected “peak blunting” effect on the probing data. Comparisonof the monoclonal and polyclonal probing ratios showed a 2.5:1 pAb*:PSA*stoichiometry (assuming a 1:1 stoichiometry inherent in the monoclonalreadout with [Ab*]

K_(D), equilibrium in binding (30), and negligible PSA “epitopedisfigurement” upon immobilization, FIG. 5E).

Discussion

1. Rapid Capture Kinetics with Efficiency Independent of AnalyteConcentration.

The reaction between the separation medium and the protein targetanalyte occurred against a background of competing reactions. In someembodiments, a portion of the photoactive BPMA sites may form conjugateswith off-target species (e.g., ampholytes, gel matrix, sorbitol, NDSB256 and CHAPS), which constitute a ˜10⁶-fold excess over proteintargets.

Consider homogeneous parallel irreversible reactions between one commonreactant (BPMA, species A) and a set of competing species (speciesB_(i)), one of which is the target protein of interest. Assuming smallcapture efficiencies, free species concentrations do not changeappreciably from their initial values, where lower case denotesconcentration of a species), meaning b_(i)˜b_(i,o). From the rate ofconsumption of BPMA, the integrated rate expression for formation of agiven adduct P_(i) can be determined:

$\begin{matrix}{p_{i} = {\frac{b_{i,o}k_{i}a_{o}}{\left( k_{T}^{\prime} \right)\left( {1 - e^{{- k_{T}^{\prime}}t}} \right)}{units}\text{:}\mspace{14mu} M\; s^{- 1}}} & \lbrack 2\rbrack\end{matrix}$Where

$k_{T}^{\prime} = {{\sum\limits_{i = 1}^{n}\; k_{i}^{\prime}} = {\sum\limits_{i = 1}^{n}\;{b_{i,o}k_{i}}}}$is a sum of the pseudo-first-order rate constants k′_(i) the competingreactions (N.B. a_(o) is the concentration of BPMA). Equation 2 showsthe property that despite each individual reaction having differentk′_(i), the rates of generation of each product are identical,characterized by a time constant

$\tau = \frac{1}{k_{T}^{\prime}}$that is made small by the strong competition for BPMA sites. Theobserved timescale of target capture was expected to be approximatelyindependent of the target protein concentration as the contribution ofk′_(target) to k′_(T) is small given the excess of off-target reactants(k′_(T)

b_(target,o)k_(target), where subscript target denotes the reactionbetween the protein target of interest and BPMA). Also, for longreaction times (from Equation 2):

$\begin{matrix}{{\eta_{target} = {{\frac{p_{target}}{b_{{target},o}} \times 100} = {\frac{k_{target}a_{o}}{k_{T}^{\prime}} \times 100}}}{\eta_{target} = {{\frac{p_{target}}{b_{{target},o}} \times 100} = {\frac{k_{target}a_{o}}{k_{T}^{\prime}} \times 100}}}{\eta_{target} = {{\frac{p_{target}}{b_{{target},o}} \times 100} = {\frac{k_{target}a_{o}}{k_{T}^{\prime}} \times 100}}}} & \lbrack 3\rbrack\end{matrix}$Again, for k′_(T)˜ independent of the target concentration b_(target,o),η_(target) is independent of (i.e., a constant across the calibrationcurve). Taken together with the fact that subsequent probe binding tocaptured target is driven to saturation at equilibrium forreaction-limited conditions and sufficiently high probe concentrationabove K_(D), a linear calibration curve was expected in the subjectmicrofluidic devices, as observed for PSA in FIG. 4B.2. Analyte Capture Efficiency is Boosted by 3D Reaction Site Matrix.

The capture efficiency of the separation medium was compared to captureon an internal surface of an “open” capillary tube with 100 μm ID. Thebenefit of high immobilization surface area A_(s) is revealed by notingthat the concentration of BPMA in a control volume V is

$a_{o} = \frac{a_{o,s}A_{s}}{V}$assuming a uniform site density a_(o,s) (mol BPMA m⁻²). Approximatingthe gel as a bundle of packed cylinders in simple cubic arrangement withradius equal to that of the mean pore radius of ˜120 nm for a 4% T, 2.6%C polyacrylamide gel yielded (via Equation 3):

$\begin{matrix}{{\frac{\eta_{gel}}{\eta_{cap}} \sim \frac{A_{s,{gel}}}{A_{s,{cap}}} \sim 300}{\frac{\eta_{gel}}{\eta_{cap}} \sim \frac{A_{s,{gel}}}{A_{s,{cap}}} \sim 300}} & \lbrack 4\rbrack\end{matrix}$Suggesting a ˜2-3 order-of-magnitude increase in capture efficiencywithin the gel matrix as compared to the capillary surface. Thisestimate was similar to the experimentally observed ˜180-fold increasein η over that measured for capillary surface photoimmobilization.3. Microscale Mass Transport Accelerates Immunoprobing to Reaction“Speed Limit”.

Probing of target protein P_(target) with antibody C electromigratingthrough the gel pores to form a stationary product immunocomplex can beconsidered as a homogeneous reaction occurring between two reactantbands mixed electrophoretically. The arrangement of target on theseparation medium circumvents the diffusion-limited mixing regime thatoften arises at the microscale. Here, the appropriate mass transfertimescale is that of band/front crossing,

$t_{cross} = {\frac{w}{u_{rel}} \sim 2}$sec for probing of a captured target band, where w is its width andu_(rsl) the velocity of the probe front.

In the case of target probing on the wall of a capillary, mass transferand surface reaction rates can become intimately coupled via a surfaceboundary layer in which the probe is locally depleted. The dimensionlessfactor that evaluates the interplay between surface reaction (ratecoefficient k′) and boundary layer mass transfer (rate coefficient β) isthe Damkohler number:

$\begin{matrix}{{Da} = \frac{k^{\prime}}{\beta}} & \lbrack 5\rbrack\end{matrix}$

Thus for Da

1, reaction speed is greater than mass transfer and the system becomesmass transfer limited, whereas for Da

1, mass transfer if faster than the reaction and the system is reactionlimited. Estimating Da for the open capillary capture scenario indicatesthat Da

1 (for the low achievable values of P_(target)), which indicates reducedboundary layer resistances in confined micro-nanoscale reaction volumes.

The small values of Da and t_(cross) suggest that the minimum reactiontimescale

$\tau_{R} \sim \frac{1}{{k_{on}c_{o}} + k_{off}}$controls the probing equilibration time, where c_(o) is the bulk probeconcentration in the separation medium or capillary lumen and k_(on) andk_(off) are the forward and reverse binding rate constants,respectively. FIG. 1F shows experimental evidence for this in theseparation medium, showing τ_(R)

t_(cross) in the separation medium. In certain embodiments, k_(on)˜10⁶M⁻¹ s⁻¹ and k_(off)˜10⁻³ s⁻¹ (K_(D)˜1 nM, depending on the antibody). Incertain cases, the probe antibody concentration c_(o) was chosen to bein large excess compared to K_(D) at c_(o)˜100 nM, giving

${\tau_{R} \sim \frac{1}{k_{on}c_{o}}} = 10$sec (c.f. t_(cross)˜2 sec). Further, at equilibrium, captured targetspecies can be shown to be saturated with probe when c_(o)

K_(D) (again contributing to assay linearity in FIG. 4B). The fact thatthe observed value of τ_(R) in the separation medium is on the order of5 min (FIG. 1F) rather than 10 sec may indicate that the kinetic “on”and “off” rates are modified in the gel environment. In some instances,the rapid mass transfer regime operating in a nanoporous separationmedium accelerates the immunoprobing process to the reaction “speedlimit”.Materials and Methods1. Microfluidic Assay Instrumentation.

Optical white soda lime glass microdevices were designed in-house andfabricated by Caliper Life Sciences (Hopkinton, Mass.) using standardwet etching processes. Channels were 10 μm in depth, 70 μm wide, and hada working length of ˜10.4 mm. Channels were spaced 80 μm apart(edge-to-edge) in doublets between each 2 mmø access well pair to ensureoptical isolation during simultaneous imaging of neighboring channels.Pairs of doublets were arranged in “imaging streets” ˜2 mm apart,yielding 4 separation media per well pair and 16 separation media perchip.

A programmable high-voltage power supply (1275 LabChip Controller,Caliper) was used for electrophoretic chip control via platinumelectrodes directly inserted into 10 μL press-fit pipet tip samplereservoirs.

Glass channels were functionalized with acrylate-terminatedself-assembled monolayers. The separation medium was fabricated viaintroduction of a gel precursor solution by capillary action. Theprecursor contained 4% w/v total acrylamide (4% T) with 2.6% of thetotal as the crosslinker bisacrylamide (2.6% C), 2% Pharmalyte 3-10titrated to pH 9.9 with NaOH (17-0456-01, GE Healthcare, LittleChalfont, UK), 3% CHAPS detergent (C9426, Sigma, St. Louis, Mo.), 10%sorbitol, 200 mM NDSB-256 (17236, Sigma), 4.5 mM BPMA (see Reagents andSamples). The initiators APS (0.08%, A3678, Sigma) and TEMED (0.08% v/v,T9281, Sigma) were added just before introduction of degassed precursorto channels. Just after visible gelation of the excess precursor, wellswere flushed and replaced with gel buffer (details of buffers used andmicrofluidic chip operation protocol are provided below).

2. Reagents and Samples.

N-[3-[(4-benzoylphenyl)formamido]propyl]methacrylamide (BPMA) monomerwas synthesized and verified by ¹H NMR and mass spectrometry. Themonomer was added to BPMA+ gel precursor solutions at 4.5 mM (˜1 mol %with respect to acrylamide) from a 100 mM stock in DMSO. BPMA−precursors contained an equivalent volume of DMSO lacking BPMA. Purifiedproteins, antibodies and fluorescent labeling protocols are described inmore detail below.

LAPC4 and DU145 lysates were purified in P-6 Bio-Spin columns (Bio-Rad,Hercules, Calif.) and added to samples at 2× dilution. Equal volumes ofa set of fluorescent IEF pI markers (pI 4.0, 4.5, 5.5, 6.2, 6.6, 7.2,7.6, and 8.7) were mixed in a cocktail and added to samples at 20×dilution (89827 and related products, Sigma). Samples in loading bufferwere titrated to pH 9.9 with 1M NaOH just prior to electrophoreticloading.

3. Data Acquisition and Analysis.

Whole channel imaging at 10× was conducted via stitching of adjacent,overlapping CCD images in ImageJ (NIH, Bethesda, Md.) to produce fullgel channel images and electropherograms. Imaging scans along bothstreets required ˜40 s to complete.

4. Synthesis of BPMA.

N-[3-[(4-benzoylphenyl)formamido]propyl]methacrylamide (BPMA,C₂₁H₂₂O₃N₂, 350.4 g mol⁻¹) monomer was synthesized via reaction of thesuccinimidyl ester of 4-benzoylbenzoic acid (BP-NHS, 323.3 g mol⁻¹;B1577, Invitrogen) with N-(3-aminopropyl)methacrylamide hydrochloride(APMA, 178.7 g mol⁻¹; 21200, Polysciences, Warrington, Pa.) in thepresence of catalytic triethylamine (TEA) in dimethylformamide (DMF). Amixture of the reactants and TEA at 50 mM each in DMF was incubatedovernight (18 hrs) at room temperature, centrifuged at 18,000 g for 5minutes and the pellet discarded. The supernatant was incubated on atube inverter for 24 hrs with 30 mg isothiocyanate-functionalized(primary amine-reactive) polystyrene beads (538604, Sigma) for every 100μmol of APMA initially added to the reaction. The mixture was then spunat 18,000 g for 5 minutes and the supernatant passed through a 0.2 μmsyringe filter. A 10-fold excess of acetone was added to the filtrateand the mixture dried in vacuo. The BPMA product (white powder) wasverified by ¹H NMR (400 MHz, d₆-DMSO, δ8.79 (t, 1H), 8.04 (t, 1H), 8.02(d, 2H), 7.80 (d, 2H), 7.75 (d, 2H), 7.70 (t, 1H), 7.58 (t, 2H), 5.67(s, 1H), 5.32 (s, 1H), 3.31 (q, 2H), 3.18 (q, 2H), 1.86 (s, 3H), 1.71(quin, 2H)) and mass spectrometry (ESI, m/z 351.2, C₂₁H₂₂O₃N₂+H⁺). 100mM stocks of BPMA in DMSO were stored at −20° C. until use, and werestable for at least 12 months.

5. Purified Proteins and Antibodies.

Pharmalyte 3-10 was minimally labeled by mixing a 1% solution in 200 mMsodium bicarbonate pH 8.3 with an equal volume of 2.27 mM CE540 in DMSO(346.5 g mol⁻¹, 15102, Active Motif, Carlsbad, Calif.; dye:ampholyteratio of ˜0.1 given average ampholyte MW of ˜500 g mol⁻¹ (1)) andincubating at 50° C. for 1 hr. wtGFP (recombinant from E. coli, A.victoria wild-type; 632373, Clontech, Mountain View, Calif.), purifiedPSA (from human seminal fluid; ab78528, Abcam, Boston, Mass.) and theServa IEF 3-10 protein marker mix (39212-01, Invitrogen, Carlsbad,Calif.) were labeled with CE540 according to manufacturer instructions.1° antibodies to PSA (goat pAb; AF1344, R&D Systems, Minneapolis, Minn.;mouse mAb; M167, CalBioreagents, San Mateo, Calif.) were labeled withAlexa Fluor 568 dye according to manufacturer instructions (Invitrogen).Fluorophore:protein molar labeling ratios, MR, were 4.0 and 4.7 for thepAb* and mAb* respectively. The rabbit anti-goat IgG 2° was labeledsimilarly (MR=3.2; 305-005-045, Jackson ImmunoResearch, West Grove,Pa.). The 1° goat pAb to GFP was prelabeled with Texas Red by themanufacturer (MR=2.9; ab6660, Abcam). Fluorescently labeled proteinswere purified using P-6 (PSA, GFP) or P-30 (antibodies) Bio-Spinchromatography columns (Bio-Rad, Hercules, Calif.) to remove free dyeprior to loading on the separation medium.

6. Buffers.

Sample loading buffer was of the same composition as gel precursor, butlacked monomers and initiators. Catholyte was 20 mM lysine, 20 mMarginine pH 10.1. Anolyte was 70 mM phosphoric acid. pH gradient washoutbuffer/probing buffer was 15 mM glycine pH 9.9, 3% CHAPS, 200 mMnondetergent sulfobetaine (NDSB) 256, 10% sorbitol.

A list of buffers used for microfluidic chip operation is provided belowin Table 1.

7. Microscopy and UV Exposure.

Chip imaging was conducted using an Olympus IX50 inverted fluorescencemicroscope equipped with CCD camera (CoolSNAP HQ², Photometrics, Tucson,Ariz.) motorized stage (Applied Scientific Instrumentation, Eugene,Oreg.) and shutter systems (Sutter Instrument, Novato, Calif.)controlled by MetaMorph software (Molecular Devices, Sunnyvale, Calif.).Flood UV duty was provided by a Hamamatsu Lightningcure LC5(Bridgewater, N.J.) directed through a Lumatec series 380 liquid lightguide (Deisenhofen, Germany) with inline UV filter (˜300-380 nmbandpass; XF1001, Omega Optical, Brattleboro, Vt.) suspended ˜10 mmabove the chip plane with UV power at chip plane of ˜160 mW cm⁻²(UV513AB meter, General Tools, New York, N.Y.). Kinetic study ofseparation medium immobilization was conducted via spot UV exposurethrough a 10× objective (Olympus UPIanFI, NA 0.3) and XF1001 exciter,with UV power at the chip plane of ˜40 mW cm⁻².

Green and red fluorescence channels were imaged at 10× using OmegaOptical filter cubes optimized for GFP (XF100-3) and DsRed2 (XF111-2).IEF pI markers were imaged prior to UV immobilization using a customUV-longpass filter cube (excitation 300-380 nm, emission>410 nm; XF1001,XF3097, Omega Optical) and channel positions were manually scored(gradient drift between focused-state marker and analyte imaging stepswas assumed to be negligible). Exposure times were 50 ms for pre-washoutscans and 400 ms post-washout, all with 4×4 pixel binning (CCD signalswere linear in exposure time). Real-time single-point imaging of GFPisoform dynamics and GFP was conducted in burst acquisition mode toeliminate camera and image transfer lag.

Transformation of fluorescence data via linear fits to pI markers andassociated data processing was performed using MATLAB scripts writtenin-house (MathWorks, Natick, Mass.). Least-squares fitting of kineticdata was performed using gnuplot software.

8. Microfluidic Chip Operation Protocol.

After gelation, access wells were filled with gel buffer (see Table 1).30 μl samples were made in loading buffer and titrated to pH 9.9 with1.5 μl 1M NaOH just prior to introduction at loading wells (˜5 μl perwell). Sample injection was performed at 200 V cm⁻¹ for 3 minutes.Catholyte and anolyte buffers were used to wash opposite wells twice;wells were subsequently filled. Focusing was conducted simultaneouslyfor the four devices in each chip (i.e., all well pairs), at 50 V cm⁻¹for 4 min; 100 V cm⁻¹, 5 min; 200 V cm⁻¹, 5 min. 3 min, 300 V cm⁻¹focusing, imaging and flood UV exposure steps were conductedindividually for each device in series. Imaging of pI markers via 50 msexposures was preceded by any green and/or red channel scans required.Following marker imaging, the chip was moved into position beneath thelightguide tip under motorized stage control. Under stopped electricfield, 2×5 s flood UV exposures were applied in neighboring spots (˜5 mmapart along the channel axis) to ensure uniform UV dosage. The finalfocusing, imaging and flood exposure steps were repeated for the otherdevices on the same chip. Refocusing and imaging was conducted asnecessary prior to simultaneous washout of all devices. Access wellswere washed and filled with glycine washout/probe buffer. Mobilizationand washout of pH gradients to the anodic wells was achieved via a 20min electrophoretic step. Labeled antibody probes were diluted inwashout/probe buffer, loaded, and removed from the separation medium in20 min electrophoretic steps; wells were washed with buffer as requiredto prevent undesired cross-reaction of 1° and 2° probes in access wells.Probe loading and washout were conducted in opposite directions tominimize non-specific signal remaining after washout. Final green and/orred scans were performed as necessary with 400 ms image exposure time.

In the case of kinetic studies of separation medium immobilization, GFPwas electrophoretically loaded at 200 V cm⁻¹ as a homogeneous stream inuntitrated loading buffer (pH˜6.5). UV exposure dosage applied via themicroscope mercury lamp was tightly controlled via the mechanicalexcitation shutter. 20 min GFP washout was performed by replacing samplewith fresh untitrated loading buffer before application of 200 V cm⁻¹field in the opposite direction to loading for 20 min.

9. Cell Culture.

The human prostate cancer cell lines DU145 and LAPC4 were obtained fromAmerican Type Culture Collection (ATCC, Manassas, Va.) and Dr. CharlesSawyers (UCLA), respectively. DU145 cells were grown in DMEM(Invitrogen) and LAPC4 cells in IMDM (Invitrogen) supplemented with 10%fetal bovine serum (FBS) (HyClone, Logan, Utah) and 100 μg/ml ofgentamycin (Fisher, Fairlawn, N.J.) in 100-mm dishes at 37° C. in 5%CO₂. Medium was changed twice a week and the cells were subculturedusing TrypLE Express (Invitrogen).

10. Lysate Preparation.

One day after feeding, three to five 100-mm dishes of DU145 cells at 90%confluency or LAPC4 cells at 75% confluency were used to prepare celllysates. Each dish was washed once with HEPES-buffered saline (HBS) andthen incubated with 1 ml of TrypLE Express at 37° C. for 5 minutes.Dishes were washed with HBS to collect cells, which were thencentrifuged to pellet the cells. After the HBS was removed, each cellpellet was resuspended in HNTG buffer (20 mM HEPES pH 7.5, 25 mM NaCl,0.1% Triton X-100, 10% glycerol). Each of these samples was thensupplemented with 1:100 Protease Inhibitor Cocktail (Calbiochem, LaJolla, Calif.) and 1 mM phenylmethylsulfonyl fluoride (Sigma). Sampleswere incubated on ice for 30 minutes, vortexing every 5 minutes. Next,samples were centrifuged at 16,000 g for 10 minutes at 4° C. The lysatesupernatant was collected and the protein concentration was measuredusing a Bio-Rad protein assay (Bio-Rad, Hercules, Calif.). Aliquots of20 μL from each lysate were frozen on dry ice and stored at −80° C.

11. Serum Preparation.

Pooled negative control serum was from US Biological (S1005-05).Advanced metastatic prostate cancer patient blood samples were collectedbetween 1998 and 1999 with informed consent under an institutionalreview board-approved protocol in red-top vacutainer tubes (BDBiosciences) at Stanford University Medical Center Oncology Clinic.Tubes were inverted five times and blood allowed to clot. Tubes werethen centrifuged at 1,000×g for 10 min. Serum was extracted and storedat −80° C. until assay.

12. Benchmark Assays.

PSA ELISAs (DKK300, R&D Systems) were conducted on LAPC4 and DU145lysates according to manufacturer instructions using a Tecan Infinitemicroplate reader (Tecan, San Jose, Calif.). ELISA calibration standardswere run in duplicate; the standard curve was linear in the 1-60 ng ml⁻¹range (R²>0.99). Unknown lysate sample were diluted in the range of20-500 fold and run in duplicate, inferred concentrations falling in thelinear calibration range were pooled as assay readout. Novex 3-10 IEFgels were run in a Novex Mini-Cell against the Serva protein marker mixaccording to manufacturer instructions with 1 μg total protein per lane;gels were silver stained with a SilverXpress kit (Invitrogen). Customslab gels were run on a Mini IEF Cell (Bio-Rad) and were of the samecomposition as the BPMA− separation medium. ε_(pHw,pHf) were determinedfor labeled analytes via fluorescence measurements in loading bufferstitrated to pH values in the range of interest and in washout buffer(FIG. 10).

Results and Discussion

1. Influence of Target Protein Hydrophobicity on Capture Efficiency.

Experiments were performed to assess the effect of fluorescence labelingof samples on the apparent capture efficiency η. The focusing andimmobilization data for CE540-labeled wtGFP* showed that CE540 labelinggenerated native and denatured protein sub-populations (FIG. 11). DuringIEF, the native population was characterized by co-localized green(endogenous) and red (CE540) fluorescence (i.e., green+, red+). Adominant GFP* population was also observed that lacked any co-localizedgreen signal (i.e., green−, red+). In this latter population of GFP*,the green fluorescence of the GFP chromophore was irreversibly destroyedupon CE540 labeling. In supporting studies, a microplate experimentshowed a 7-fold reduction in green fluorescence of GFP* from that of GFPin an isoelectric ampholyte buffer, providing further evidence forlabeling-induced denaturation (see FIG. 10).

Experiments performed on the photoimmobilization efficiencies offluorescently labeled proteins indicated that the native GFP* populationshowed a η_(green) based on native green fluorescence of 10.1%, whilethe denatured GFP* segment gave η_(red) based on its red CE540 signal of34.5% (see Table 2). Taken together, the high 34.5% value describedimmobilization of an unfolded form of GFP that may be prone to a greaterdegree of hydrophobic “pre-covalent” interactions with the benzophenonemoieties in the gel matrix. This is consistent with the observation thatminor conformational increases in solvent-accessible surface area ofprotein targets produced disproportionately large increases indiazirine-mediated photolabeling efficiency, suggesting higherprotein-label affinity for looser protein conformations.

2. Benchmark Macroscale IEF Slab Gels.

Experiments were performed to compare the PSA and GFP readouts in thesubject microfluidic device to those of a conventional Novex pH 3-10 IEFslab gel (FIG. 12). Slight differences between the microfluidic deviceand conventional Novex assays of PSA were mitigated using a custom slabgel with the same buffer composition as the microfluidic device. Incontrast, the GFP isoforms arising by differential C-terminalproteolytic cleavage exhibited similar behavior in the chip and Novexgels. This comparison study suggested that the isoform pattern of PSAwas sensitive to the presence of the solubilizing additives used inmicrofluidic device (CHAPS, sorbitol and NDSB-256) that may modulate PSAglycan solvation.

3. Probe Binding Stoichiometry.

Based on antibody probing analyses for purified PSA, the stoichiometryof secondary:primary Ab* binding can be inferred from the ratio of therespective fluorescence traces (FIGS. 4B and 4C). The degrees oflabeling of each antibody probe were similar, and the labeling dye wasthe same (red Alexa Fluor 568). The binding stoichiometry was determinedto be approximately 2.5 across the relevant pH range, exhibitingsomewhat higher values at the acidic end of the isoform pattern due to anonspecific contribution of the secondary Ab* to the assay readout.

4. Assays in Isoform “Affinity Mapping” Mode.

Experiments were performed to validate the capability of themicrofluidic assay to measure immunoreagent isoform specificity. Theisoform distribution of IEF-focused CE540-labeled PSA* was compared tothe fluorescence readout after photoimmobilization and probing with mAb*and pAb* (FIG. 5). Alignment between each pair of fluorescence intensityprofiles (PSA*, Ab*) was accomplished by applying a translation inferredfrom their cross-correlation. The translational shift corrected for theslight drift (ca. 190 μm) between imaging of focused PSA* and thephotoimmobilization step. The focused PSA* isoform pattern agreed wellwith that of the probed unlabeled PSA, suggesting a minimal effect ofCE540 on the pI values of the native PSA isoforms (compare FIGS. 5A and5B and FIG. 4A). Ratiometric comparison of the probed and focused PSA*signals suggested spatially uniform probe layering onto immobilized PSA*across the pH region of interest, for both polyclonal and monoclonaldetection antibodies (FIGS. 5C and 5D). Some apparent variation acrossthe pH range was induced by diffusional band broadening duringphotoimmobilization, which had the expected “peak blunting” effect onthe probing data. Comparison of the monoclonal and polyclonal probingratios showed a 2.5:1 pAb*:PSA* stoichiometry (FIG. 5E, assuming a 1:1stoichiometry inherent in the monoclonal readout with [Ab*]>>K_(d),equilibrium in binding, and negligible PSA “epitope disfigurement” uponimmobilization).

5. Target Antigen Immobilization Kinetics.

The reaction between BPMA and the protein target of interest occurredagainst a background of competing reactions. In some cases, a portion ofthe BPMA sites formed conjugates with off-target species, such as theampholytes, gel matrix, sorbitol, NDSB 256 and CHAPS. The combinedconcentration of these off-target species was >20% wt/vol in theseparation medium precursor, constituting a ˜10⁶ fold excess overprotein targets in the normal device operating regime. A kinetic schemethat characterized the capture efficiency of a protein target in thisregime was developed. Consider parallel irreversible reactions betweenone reactant (BPMA, species A) and a set of competing species (speciesB_(i)), one of which is the target protein of interest. The reactionscheme is as follows:

For low capture efficiencies η, it can be assumed that the free speciesconcentrations do not change appreciably from their initial values, i.e.b_(i)˜b_(i,o) (lower case denotes concentration of a species). The rateof disappearance of BPMA is thus:

$\frac{da}{dt} = {{- k_{T}^{\prime}}a}$Where

$k_{T}^{\prime} = {{\sum\limits_{i = 1}^{n}\; k_{i}^{\prime}} = {\sum\limits_{i = 1}^{n}\;{b_{i,o}k_{i}}}}$is a sum of the pseudo-first-order rate constants k′_(i) of thecompeting species.Integrating this expression gives:a=a _(o) e ^(−k′) ^(T) ^(t)  [1]For generation of a given product P_(i):

$\begin{matrix}{\frac{{dp}_{i}}{dt} = {b_{i,o}k_{i}a}} & \lbrack 2\rbrack\end{matrix}$Substituting Equation 1 into Equation 2 and integrating gives:

$\begin{matrix}{{\int_{0}^{p_{i}}\ {dp}_{i}} = {\left. {b_{i,o}k_{i}a_{o}{\int_{0}^{t}{e^{{- k_{T}^{\prime}}t}\ {dt}}}}\Rightarrow p_{i} \right. = \frac{b_{i,o}k_{i}a_{o}}{\left( k_{T}^{\prime} \right)\left( {1 - e^{{- k_{T}^{\prime}}t}} \right)}}} & \lbrack 3\rbrack\end{matrix}$This result reveals the property that despite each individual reactionhaving different pseudo-first-order rate constants (k′_(i)=b_(i,o)k_(i))the product generation rates are identical and are characterized by atime constant

$\tau = {\frac{1}{k_{T}^{\prime}} = {\frac{1}{\sum\limits_{i = 1}^{n}\;{b_{i,o}k_{i}}}.}}$In certain instances, k′_(T)

b_(target,o)k_(target) (subscript target denotes the reaction betweenthe protein target of interest and BPMA), i.e. that the contribution ofk′_(target) to k′_(T) is small given the large excess of off-targetspecies in the reaction. As such, the observed reaction rate is expectedto be approximately independent of the target protein concentration.Thus, the observed separation medium immobilization time constant isexpected to be invariant across the target calibration curveconcentration range.For long reaction times (t→∞), from Equation 3:

$\begin{matrix}{p_{target} = {\left. \frac{b_{{target},o}k_{target}a_{o}}{k_{T}^{\prime}}\Rightarrow\eta \right. = {{\frac{p_{target}}{b_{{target},o}} \times 100} = {\left. {\frac{k_{target}a_{o}}{k_{T}^{\prime}} \times 100}\Rightarrow\eta \right. = {{\frac{p_{target}}{b_{{target},o}} \times 100} = {\frac{k_{target}a_{o}}{k_{T}^{\prime}} \times 100}}}}}} & \lbrack 4\rbrack\end{matrix}$Again, for k′_(T) approximately independent of b_(target,o), theseparation medium capture efficiency is also expected to be independentof b_(target,o) (i.e., constant across the calibration curve). Further,increased k_(target), increased a_(o) (increased [BPMA]), or decreasedk_(T) (decreased concentration of competing species and/or rates ofcompeting reactions) all increase η.

Given that the immobilized target concentration is expected to be aconstant fraction of the nominal concentration, and that probesaturation of captured target is guaranteed across the calibration curveat equilibrium for Da

1 and sufficiently high probe concentration above K_(D), a linearcalibration relationship in the microfluidic system was expected and wasobserved in the experimental data for PSA.

The benefit of high immobilization surface area is shown by consideringthe volumetric concentration of BPMA, a_(o) given a consistent sitedensity a_(o,s) distributed across an immobilization surface withsurface area to volume ratio of

$\begin{matrix}{{\frac{A_{s}}{V}\text{:}\mspace{14mu} a_{o}} = \frac{a_{o,s}A_{s}}{V}} & \lbrack 5\rbrack\end{matrix}$Substituting Equation 5 into Equation 4 determines a ratio of gel toopen capillary capture efficiencies:

$\begin{matrix}{\frac{\eta_{gel}}{\eta_{cap}} = \frac{\frac{A_{s,{gel}}}{V}}{\frac{A_{s,{cap}}}{V}}} & \lbrack 6\rbrack\end{matrix}$The gel surface area A_(s,gel) can be compared to an open capillaryA_(s,cap) by approximating the gel structure to be a bundle of packedcylinders in simple cubic arrangement with radius r_(gel) equal to thatof the mean pore radius of 120 nm for a 4% T, 2.6% C gel (8), giving:

A s , gel V ∼ 2 ⁢ ⁢ π ⁢ ⁢ r gel ⁢ l ( 2 ⁢ ⁢ r gel ) ⁢ 2 ⁢ l = π 2 ⁢ ⁢ r gel$\frac{A_{s,{cap}}}{V} = {\frac{2\;\pi\; r_{cap}l}{\pi\; r_{cap}^{2}l} = \frac{2}{r_{cap}}}$From Equation 6:

${\frac{\eta_{gel}}{\eta_{cap}} \sim \frac{\pi\; r_{cap}}{4\; r_{gel}}} = 327$With r_(cap)=50 μm.

A ˜2-3 order-of-magnitude increase in capture efficiency was expectedwithin the gel matrix as compared to the capillary surface, which wasconfirmed by experimental observation of an ˜180-fold improvement in ηover that observed from a capillary surface.

6. Probe Binding to Immobilized Antigen.

Experiments were performed to compare the timescales of probe masstransfer and binding for a target analyte (P_(target)) immobilized tothe wall of an open capillary or to the separation medium. In thefollowing analysis, gel and free solution antibody probe diffusivitiesof ˜4.5×10⁻¹² and ˜3.4×10⁻¹¹ m² s⁻¹ respectively were used. Thecapillary tube length y in the open-channel case was the approximatelength of an immobilized target peak (˜100 μm) with tube diameter 100μm. The surface concentration of target antigen, P_(target), was thatresulting from attachment of focused analyte at η=1% from a 100 nMnominal solution assuming an IEF concentration factor of ˜

${\sim\frac{10.4\mspace{14mu}{mm}}{0.1\mspace{14mu}{mm}}} \sim 100$onto a surface area arising from the cylindrical pore model alreadydescribed. This gives P_(target)=7.6×10⁻¹² mol m⁻². For equivalence ofthe two cases, the same P_(target) for the open capillary was assumed.The values of k_(off)˜10⁻³ s⁻¹ and k_(on)˜10⁶ M⁻¹ s⁻¹ for Ab-Aginteractions.

Consider an immobilized antigen target P_(target) attached to acapillary wall and probed with a detection antibody C to form astationary complex X:

To determine when mass transfer limitation of the reaction timescalewill occur due to probe depletion near the reaction surface, the rateequation for immunocomplex formation at the surface is:

$\begin{matrix}{{\frac{dx}{dt} = {{k_{on}c_{s}p_{target}} - {k_{off}x}}},{{units}\text{:}\mspace{14mu}{mol}\mspace{14mu} m^{- 2}s^{- 1}}} & \lbrack 7\rbrack\end{matrix}$Where c_(s) is the surface concentration of probe, which is equal to thebulk probe concentration c_(o) under conditions of reaction limitation,but is between zero and c_(o) where mass transfer (by convection at theedge of a boundary layer and diffusion through this layer) to thesurface is limiting. Neglecting the “off” term in x, the surface flux ofprobe {dot over (n)}_(c) _(s) is:

$\begin{matrix}{{\overset{.}{n}}_{c_{s}} = {{- \frac{dx}{dt}} = {{- k_{on}}p_{target}c_{s}}}} & \lbrack 8\rbrack\end{matrix}$

Low probe concentration compared to captured target allowed thepossibility of mass transfer limitation on surface flux of probe. Thus,P_(target) (mol m⁻²) may be combined with k_(on) (M⁻¹ s⁻¹) into apseudo-first-order rate constant k′ (standard units of ms⁻¹):{dot over (n)} _(c) _(s) =−k′C _(S) , k′=k _(on) P _(target)  [9]

This simplified kinetic is sufficient to demonstrate the effect of masstransfer resistance in the surface boundary layer on the apparent rateof immunocomplex formation. For convection, diffusion and reaction undersimplifying assumptions that the probe is not depleted at the edge ofthe boundary layer, and that the probe diffusion profile is at steadystate (linear c between and c_(o)), it can be shown that:

$\begin{matrix}{{\overset{.}{n}}_{c_{s}} = {- \frac{k^{\prime}c_{o}}{\left( {1 + \frac{k^{\prime}}{\beta}} \right)}}} & \lbrack 10\rbrack\end{matrix}$Essentially the probe consumption at the surface depends on a bulkreaction rate k′c_(o) adjusted by a factor

$\left( {1 + \frac{k^{\prime}}{\beta}} \right)$accounting for mass transfer resistance in the boundary layer, where βis the mass transfer coefficient (ms⁻¹). The dimensionless factor thatevaluates the interplay between reaction and mass transfer is theDamkohler number:

$\begin{matrix}{{Da}_{1} = \frac{k^{\prime}}{\beta}} & \lbrack 11\rbrack\end{matrix}$Thus for Da₁

1, the reaction speed is greater than mass transfer and the system ismass transfer limited with apparent rate

${{\overset{.}{n}}_{c_{s}} = {{- \frac{dx}{dt}} = {{- \beta}\; c_{o}}}};$whereas for Da₁

1, mass transfer is greater than the reaction speed and the system isreaction limited with apparent rate

${\overset{.}{n}}_{c_{s}} = {{- \frac{dx}{dt}} = {{- k^{\prime}}c_{o}}}$${\overset{.}{n}}_{c_{s}} = {{- \frac{dx}{dt}} = {{- k^{\prime}}.}}$

The mass transfer coefficient β is a component of the Sherwood number Sh(a mass transport analog of the Nusselt number in heat transfer), whichcan be estimated from empirical relations determined for different flowproperties and interface geometries.

$\begin{matrix}{{{{Sh} = {\frac{\beta\; l}{D} = \frac{{mass}\mspace{14mu}{transfer}\mspace{14mu}{velocity}}{{diffusion}\mspace{14mu}{velocity}}}},{where}}{I\mspace{14mu}{is}\mspace{14mu} a\mspace{14mu}{characteristic}\mspace{14mu}{length}\mspace{14mu}{in}\mspace{14mu}{the}\mspace{14mu}{{system}.}}} & \lbrack 12\rbrack\end{matrix}$For the open capillary case, an accurate (within ˜1%) relationship forlaminar flow in a cylindrical tube is readily available:

$\begin{matrix}{{Sh} = {\frac{\beta\; d}{D} = {1.62\left( \frac{d^{2}u}{yD} \right)^{\frac{1}{3}}}}} & \lbrack 13\rbrack\end{matrix}$Where d is the tube diameter, y the tube length (length of the reactionzone), u the average velocity in the tube and D the diffusivity of theprobe in free solution.

Equations 11 and 13 give Da₁<1 for probe flowrates greater than u˜1 mms⁻¹. Further decreases in Da₁ occur relatively “slowly” with increasesin u due to the cube root dependence of Sh on u. However, given thatη˜0.01% would be more reasonable in the open capillary case, Da₁

1, and thus the probing step is reaction rather than mass transferlimited.

For probing in the microfluidic device, the target antigen isdistributed throughout the channel volume, suggesting that probe driventhrough the gel pores reacts with captured antigen in a homogeneousfashion (i.e., no boundary layer resistance exists). An alternativeDamkohler number has been posited for such electrophoretic “bandcrossing” reactions:

$\begin{matrix}{{Da}_{2} = \frac{t_{cross}}{\tau_{R}}} & \lbrack 14\rbrack\end{matrix}$Where

$t_{cross} = \frac{w}{u_{rel}}$is the time required for the probe front to sweep through the capturedband, which is ˜2 sec given an observed probe velocity of u_(rel)˜50μms⁻¹ in the separation medium and a target band width w=100 μm.Reaction-limited conditions (Da₂

1) was also expected in this framework given the experimentalobservation that t_(cross)

τR (see FIG. 1F).

Da_(1,2)

1 such that the relevant probe transport timescale is substantiallysmaller than the reaction timescale (i.e., mass transfer is faster thanthe reaction). Thus, the binding reaction at the surface may be focusedon depletion of captured target as it is occupied by relativelyunconstrained delivery of probe:

$\begin{matrix}{{\frac{dx}{dt} = {{k_{on}c_{s}p_{target}} - {k_{off}x}}},} & \lbrack 15\rbrack\end{matrix}$This equation is identical to Equation 7, but c_(s)˜c_(o) andP_(target)=(P_(target,total)−x) where P_(target,total) is the totalconcentration of immobilized target. Thus:

$\begin{matrix}{{\frac{x(t)}{p_{{target},{total}}} = {\frac{\frac{c_{o}}{K_{D}}}{1 + \frac{c_{o}}{K_{D}}}\left( {1 - e^{{- {({{k_{on}c_{o}} + k_{off}})}}t}} \right)}}{for}{{Da}_{1,2}{\operatorname{<<}1}}} & \lbrack 16\rbrack\end{matrix}$Where

$K_{D} = \frac{k_{off}}{k_{on}}$is the equilibrium dissociation constant for the Ab-Ag interaction.

The bulk probe antibody concentration c_(o) was in large excess comparedto K_(D) at c_(o)>100 c_(o)>100 nM, giving

${\tau_{R} \lesssim \frac{1}{k_{on}c_{o}}} = 10$${\tau_{R} \lesssim \frac{1}{k_{on}c_{o}}} = 10$sec (t_(cross)

τ_(R), as observed experimentally), and at equilibrium

$\frac{x(t)}{p_{{target},{total}}} = {\left. \frac{\frac{c_{o}}{K_{D}}}{1 + \frac{c_{o}}{K_{D}}} \right.\sim 1}$(i.e., probe binding saturates captured target).7. Determination of Free Solution and in-Gel Diffusivities.

The diffusion coefficient for GFP in 4% T, 2.6% C polyacrylamide gel wasdetermined by defocusing to be 2.05×10⁻⁷ cm² s⁻¹ (FIG. 3A). Thediffusion coefficient for a given protein in a polyacrylamide matrix canbe estimated via an adjusted Stokes-Einstein diffusivity:

$\begin{matrix}{r_{H} = {0.595\mspace{14mu}\left( M_{W} \right)^{0.427}}} & \lbrack 17\rbrack \\{D = {\frac{k_{B}T}{6\;\pi\;\mu\; r_{H}}e^{{- k_{c}}r_{H}\varphi^{0.75}}}} & \lbrack 18\rbrack\end{matrix}$r_(H) is the protein hydrodynamic radius, M_(w) the protein molecularweight in kDa, k_(E) is Boltzmann's constant, T temperature, μ theviscosity of the medium (μ˜1.26×10⁻³ Pa·s for a 10% sorbitol solution(17)), k_(c)=0.45 Å⁻¹, φ the polymer volume fraction.

This relationship gives a diffusivity of GFP in 4% T, 2.6% Cpolyacrylamide gel of ˜2.5×10⁻⁷ cm² s⁻¹, which is within 20% of thevalue measured by defocusing (2.05×10⁻⁷ cm² s⁻¹). Thus, the diffusivityfor a probe antibody can be estimated by similar means to be ˜4.5×10⁻⁸cm² s⁻¹ in the gel and ˜34×10⁻⁷ cm² s⁻¹ in free solution.

TABLE 1 Buffers used, all % values are w/v unless stated otherwise. Vol(μl) Component Final Gel Precursor (BPMA+) 56.3 26.7% CHAPS 3% 66.7 1.5MNDSB 256 200 mM 62.5 80% sorbitol 10% 66.7 30% T, 2.6% C (37.5:1 premix)4% T, 2.6% C 40 Pharmalytes 3-10 pH 9.9 2% (25%) 22.5 100 mM BPMA inDMSO 4.5 mM BPMA, 4.5% DMSO v/v 177.3 DI H₂O 4 10% APS 0.08% 4 10% TEMEDv/v 0.08% v/v Total 500 Loading Buffer 112.5 26.7% CHAPS 3% 133.3 1.5MNDSB 256 200 mM 125 80% sorbitol 10% 55.6 Pharmalytes 3-10 (36%) 2% 45DMSO 4.5% v/v 478.5 DI H2O Total 950 Catholyte 168.8 26.7% CHAPS 3% 2001.5M NDSB 256 200 mM 187.5 80% sorbitol 10% 150 10x Novex catholyte 1x(20 mM lysine, 20 mM arginine) 67.5 DMSO 4.5% v/v 726.2 DI H2O Total1500 Anolyte 1500 10x Bio-Rad anolyte 10x (70 mM H₃PO₄) Total 1500 GelBuffer 112.5 26.7% CHAPS 3% 133.3 1.5M NDSB 256 200 mM 125 80% sorbitol10% 80 Pharmalytes 3-10 pH 9.9 2% (25%) 45 DMSO 4.5% v/v 504 DI H2OTotal 1000 Washout/Probe Buffer 168.8 26.7% CHAPS 3% 200 1.5M NDSB 256200 mM 187.5 80% sorbitol 10% 22.5 1M glycine NaOH pH 9.9 15 mM glycine67.5 DMSO 4.5% v/v 853.8 DI H2O Total 1500

TABLE 2 Capture efficiencies η (%) under focusing conditions.CE540-labeling indicated by “*”, fluorescence emission channel used todetermine η denoted by “green” and “red”. Target pH η_(green) η_(red)GFP ~5.2 1.30 ± 0.17 (n = 44) — GFP* ~5.2 10.1 ± 1.91 (n = 8)  34.5 ±3.04 (n = 8) PSA* ~6.5 — 9.92 ± 0.86 (n = 3) Pharmalyte 3-10* 5.0 — 7.17± 1.95 (n = 4) 7.5 — 13.3 ± 1.70 (n = 4)

Example 2

The subject microfluidic device can be used to perform size basedseparations linked to immunoprobing in both native and SDS-PAGEvariants. Embodiments that include size based separation (SDS-PAGE) andimmunoprobing may facilitate a microfluidic “western blot”. Experimentswere performed that show native (FIG. 13) and SDS-PAGE (FIG. 14)separations of Alexa Fluor 488-labeled fluorescent protein ladderspecies with subsequent photocapture onto the separation medium andin-situ probing for ovalbumin (OVA*) with a specific antibody labeledwith Alexa Fluor 568. The assay was performed with unlabeled targetanalytes, and was directly analogous to Western blotting, withsignificantly reduced assay time, reagent and sample requirements ascompared to typical Western blotting.

The first separation step was performed across a discontinuouspolyacrylamide interface built using two-step chemical polymerization ofa high percentage (6% T) separation gel precursor (BPMA+) and a lowpercentage (3.5% T) loading gel precursor (BPMA−). The high percentageprecursor was chemically polymerized against an air interface at amicrofluidic cross-channel injection T.

Once the high percentage separation gel was polymerized, the lowpercentage precursor solution was added, wetting directly against theseparation gel interface at the injection T. The low percentage solutionwas then polymerized chemically as well, forming a discontinuousseparation gel analogous to those used in macroscale polyacrylamide slabgels.

After timing and recording an initial separation, the second separationwas performed, at which point the E field was stopped and UV lightapplied via a 4× microscope objective. Washout of excess protein wasdone rapidly directly after capture. The captured ladder profile wasrepeatable, with capture efficiencies of approximately 50%, regardlessof species identity. Introducing and washing out the fluorescentantibody for ovalbumin produced quantitative detection duty in bothnative (FIG. 13) and SDS-PAGE (FIGS. 14 and 16) assay versions.

A single-microchannel approach was also developed that allowed the sameSDS-PAGE separation to be performed in a reduced complexity device thatincluded two (rather than four) access wells. Sample stacking wasachieved by transient isotachophoresis followed by a zoneelectrophoresis process in direct series (FIG. 15). In some embodiments,sample stacking improved band resolution, improved assay sensitivity andremoved the need for T-injection. A similar separate-capture-probestrategy then allowed multiplexed analyte detection (FIG. 16, fourproteins probed simultaneously). Analyte sizing conformed to theexpected log-linear relationship between protein molecular weight andmigration distance in the device (FIG. 17).

Example 3

Experiments were performed using a microfluidic device according toembodiments of the present disclosure for western blotting. In certainembodiments, the assay duration was reduced from 3-18 hours to 10-60 minas compared to typical western blotting. In some instances, 5-plexsimultaneous analyte detection and quantitative readout was performed.In a single microchannel, the subject microfluidic device performedstacking sodium dodecyl sulfate-polyacrylamide gel electrophoresis(SDS-PAGE), protein immobilization with SDS removal (blotting), andsubsequent antibody probing. The scalable, high-throughput nature ofmicrofluidic design allowed 54-plex parallelization, and 10 min assaytimes. A photopatternable (blue light) and photoreactive (UV light)polyacrylamide gel forms the separation medium for the assay. Thepolymer included both an SDS-PAGE separation matrix with a definedstacking interface and, after brief UV-switching, a proteinimmobilization matrix offering high capture efficiencies (>75%,obviating blocking). Experiments were performed to analyze NFκB in 293Tcell lysate yielding femtogram sensitivities (tens of transfected cellsper 3 μl sample). Antibody requirements were typically <1 ng per blot,which represented a 1.000-fold reduction over conventionalimmunoblotting. Experiments were performed to validate a rapidconfirmatory HIV diagnostic requiring <1 μl of human serum using p24 andgp120 bait antigens.

Results and Discussion

Dual Band-Tunable PACTgel for Protein Separations and Capture.

Microchannels were filled with a dual spectral band photoactive proteincapture gel with tunable porosity separation and blotting polymer (FIG.18A). Using microfluidic integration and the functional polymer, allsteps from isotachophoretic (ITP) stacking during sample injection toweight-based separation of denatured protein analytes (SDS-PAGE, FIG.18B) to immunoblotting with fluorescently labeled primary and secondaryantibodies were performed in one microfluidic channel in 10-60 min. Thepolyacrylamide-based separation medium was built using ariboflavin-driven photopolymerization strategy that preserved aspectrally distinct UV light-responsive capture functionality of thegel. Photochemically fabricated separation media were patterned usingblue light via photomask exposure to provide fine spatial control overgel porosity and sieving interface position (coefficient of variation,CV, of 3.5%, n=60). Control of gel porosity may facilitate assayrepeatability across the full 54-channel implementation. Separationmedia were also optimized for quantitative protein analyte capturefollowing SDS-PAGE separations (>75% capture efficiencies for allanalytes) with UV exposure times of 45-60 s applied via a 4× microscopeobjective (FIG. 18C). Due to the benzophenone-functionalized,light-activated character of the gel, no separate blocking steps wereneeded after protein immobilization. Simultaneous probing of 5 analytespecies was performed using antibody cocktails applied in a singleelectrophoretic step (FIG. 18D).

Micro-Western Blot Assay Design.

In some embodiments, microfluidic chips for micro-Western blot included4 sample throughput in technical triplicate (FIG. 19A). Parallelizationwas scalable by altering the number of chips interfacing with theelectrode array. As shown in FIG. 19B, 54 microchannel throughput (18samples) was performed, with increased throughput achievable withadjustment to the UV exposure and electrical connectivity hardware.Channels included one access well pair per triplicate blot, and channelwidths were 70 μm. Between-device peak area CVs for identical samplesprobed simultaneously for ovalbumin (OVA) and β-galactosidase (β-gal)were 25% each, with the ratio of their peak areas varying with a CV of14.7%. The measured reproducibility and use of internal migrationcontrols allowed data comparison across devices and chip modules. Inaddition to the stacking gel pore-size discontinuity employed here fortransition from ITP to SDS-PAGE, spatial control over gel porosityallowed formation of e.g., separation gels with gradients in pore size.

Micro-Western Blot Readout Modes.

Experiments were performed to test three methods of analyte detection.In some instances, dynamic imaging of fluorescent antibody probeaccumulation at the site of captured analytes was performed. Thisdynamic imaging approach yielded a primary antibody probing timeconstant of 8.2 min for a roughly 1 μM OVA band captured on theseparation medium after SDS-PAGE (FIG. 19C). Probe waselectrophoretically introduced 4 min after the start of the assay, andrequired ˜1 min to migrate through the gel pores to the immobilized OVAband. A probe band SNR of >10 was recorded for a 10 min total assaytime. In some cases, the rapid probing kinetics may be due toelectrokinetic through-pore probe delivery that is not significantlyimpeded by surface boundary layer diffusion resistances. Dynamicmonitoring of target peak SNR achieved an acceptable readout signal andassay time.

Experiments were also performed using both primary and secondaryfluorescently labeled antibody probes and an endpoint readout withwashout of excess probe. This approach resulted in higher SNRs over thefull separation range while still maintaining relatively rapid assaytimes of less than 60 min (FIG. 18D and FIG. 19B).

Experiments were also performed to achieve a high-sensitivity detectionmethod using enzyme-amplified secondary antibody detection. An alkalinephosphatase-conjugated secondary antibody and a charged fluorogenicsubstrate (6,8-difluoro-4-methylumbelliferyl phosphate or DiFMUP, FIG.19D) suitable for electrophoretic introduction into separationmedium-filled microchannels was used.

High Resolution Single Microchannel SDS-PAGE.

A transient-ITP buffer arrangement using a tris-glycine SDS-PAGE systemwas used as the first assay stage (FIG. 18B). During the stacking phase,a diffuse plug of protein injected at the microchannel entrance waselectrophoretically compacted into an ˜200 μm zone prior toelectromigration across a sharp sieving gel interface (a 7.5% T sievingseparation medium at ˜400 μm into the microchannel). Proteinelectromigration through the gel interface caused a transition fromtransient ITP to SDS-PAGE, as the trailing glycine electrolyte overtookthe stacked protein zones. Stacking achieved >2-fold samplepreconcentration and minimized injection dispersion, increasing analyteresolution during the sieving phase. In this implementation, bandordering in the stack was not necessarily governed by molecular weightduring ITP, thus, in some instances, dynamic band reordering wasobserved during the brief transition from ITP to PAGE (see band “x” inFIG. 18B).

On-chip SDS-PAGE yielded a log-linear molecular weight versus migrationdistance relationship (R²>0.98 for MW marker proteins), providingreliable sizing over the 20-150 kDa analyte range. The sieving gelformulation was tunable for enhanced resolution over specific weightranges of interest. Immobilized peaks with differences in weight of >19%were resolvable (separation resolution R_(s)≥1). This micro-Westernstacking and sizing performance resulted in a resolution competitivewith both conventional slab-gel and capillary western blotting systems.However, the micro-Western system achieved these results in a 3 mmseparation distance; >10-fold shorter than either conventionaltechnique. Minimized separation distances resulted in a decrease inassay time during SDS-PAGE, which typically requires 60 s to completeon-chip, a 40- to 90-fold reduction in time as compared to conventionaltechniques.

Rapid, High Efficiency Analyte Blotting by Photocapture.

Directly following SDS-PAGE a 60 s or less exposure to UV lightactivated protein capture on the channel-filling separation medium.Pendant benzophenone groups built into the polyacrylamide gel scaffoldvia a methacrylamide comonomer(N-[3-[(4-benzoylphenyl)formamido]propyl]methacrylamide, BPMAC)underwent hydrogen abstraction and covalent coupling to nearbybiomolecules via a radical mechanism. The separation medium captureefficiencies of fluorescently-labeled marker proteins (assayedsimultaneously with unlabeled target proteins) for a 45 s UV exposureperiod were measured and found to be: 107.9±0.6%, 85.4±3.5%, 103.4±3.8%,and 75.2±0.8% for β-gal (116 kDa), bovine serum albumin (BSA, 66 kDa),OVA (45 kDa) and trypsin inhibitor (TI, 21 kDa), respectively (all±SD,n=3, respective within- and between-device coefficients of variation of<5% and <20% for each band, FIG. 18C).

High capture efficiencies were maintained for protein concentrations ofat least 100 pg nl⁻¹ (˜10⁹ proteins nl⁻¹) due to an excess ofbenzophenone capture sites (˜10¹² sites nl⁻¹) distributed throughout theseparation medium. In contrast, a BPMAC-negative control separationmedium lacking capture sites exhibited negligible protein blotting (FIG.18C). High capture efficiency after SDS-PAGE may be due to analytedenaturation. Denaturation may expose buried protein residues to thesieving matrix, thus promoting hydrophobic interactions between theunfolded analytes and the pendant separation medium benzophenone groups.In some cases, the reduced requirement for protein solubilizing agents(e.g., detergents) in SDS-PAGE as compared to IEF may reduce stericbarriers to productive coupling. The 75-100% separation medium captureefficiency range was comparable to conventional electrotransfer blottingefficiencies on polymer membranes and was a 10.000-fold improvement overconventional capillary surface-capture (0.01% for green fluorescentprotein). Completion of analyte capture in 60 s was a ˜90-fold increaseover typical membrane electrotransfer timescales in conventional benchtop western blotting.

Characterization of chemically and photochemically fabricated separationmedia showed a sigmoidal dependence of fluorescently labeled BSA captureefficiency on UV exposure time (FIG. 18C). The low capture efficienciesobtained for exposure times of less than ˜20 s may be due to an initialinhibitory phase caused by scavenging of reactive benzophenone sites bydissolved oxygen prior to a productive phase of analyte capture onto theseparation medium. The capture time courses for the two separation mediaformulations were substantially identical, with complete BSA capturemeasured in each for UV exposure times of greater than ˜45 s. Thisresult confirmed that the use of blue light with a wavelength ofapproximately 470 nm for spatially directed, photochemical separationmedium fabrication does not compromise subsequent protein analyteblotting.

Enzyme-Amplified Micro-Western Blot Readout.

Following photocapture, analyte bands were probed withfluorescently-labeled primary and secondary antibodies via activeelectrophoretic introduction and washout from the nanoporous separationmedium. Use of an enzyme-amplified assay detection protocol yielded SNRincreases of >100-fold in a 10 s reaction time at a ˜1 μM β-gal analyteband (FIG. 19D). This increase may be due to in situ conversion of acharged DiFMUP substrate by an alkaline phosphatase-conjugated secondaryantibody. The blue fluorescent DiFMU product diffused away from theproduction site even under stopped (floating) electric field, presentinga tradeoff between the amplification factor and the separationresolution of the blot. In certain embodiments, precipitatingphosphatase substrates may minimize this tradeoff.

Quantitative Micro-Western Blots with Gold-Standard Validation.

To validate the microfluidic western blot, experiments were performed toassay for the transcription factor NFκB (p105, p50) in lysate from anNFκB-transfected 293T cell line (FIG. 20A). A primary and afluorescently-labeled secondary antibody were employed forimmunoprobing. Assays of NFκB transfected lysate and untransfectednegative controls yielded similar probing patterns in on-chip andconventional formats. In addition to conventional GAPDH probing,measurement of the total injected zone fluorescence for the weightladder proteins was a useful loading control in micro-Western assays.

Experiments were performed to assay for several purified humanimmunodeficiency virus (HIV) proteins (FIG. 20B). The weights of themajor bands of viral reverse transcriptase and the envelope glycoproteingp120 determined from micro- and conventional slab-gel western blottingagreed to within 12%. Within-device CVs for all bands were <2% (n=3 foreach). Minor bands for both gp120 (56, 40 kDa) and p24 (49 kDa) observedonly on conventional western blots were likely attributable to thefactors that differ between the macro- and microscale workflows,including differences in blotting efficiency, in the SDS-PAGE andprobing buffer systems, and in the degree of analyte renaturation priorto immunoprobing.

Quantitative micro-Westerns were achieved over a linear dynamic range of2.1 logs with a 5 nM LOD for gp120 (FIG. 20C); on par withenzyme-amplified chromogenic signal development in conventional westernblots. The average within-device peak area CV across the calibrationcurve data of FIG. 20C was 14% (n=11 points). The NFκB p105 LOD wasreached at 128-fold dilution of a 0.5 mg ml-1 lysate, corresponding tothe total protein mass from ˜60 transfected mammalian cells in the 3 μlsample volume. Stated another way, the detected analyte mass represented<1% of the mass of a single cell on the basis of the 0.2 nl volumeinjected into each microchannel. These detection limits were achieved inthe micro-Western blot without use of amplified detection. Themicro-Western LOD of 1.2 ng per 3 μl sample or 70 fg of gp120 per 0.2 nlinjected volume implied the ability to detect 25,000 virus particles ona gp120 basis (4-35 copies per virion), or as few as 100 particles forp24 (5,000 copies per virion). Concentration-based LODs may be reducedby 2-3 orders of magnitude, for example by using enzyme-amplification(see FIG. 19D).

Micro-Western blotting consumed <1 ng of each antibody, in contrast with˜1 μg consumed in conventional western blotting. Similarly, the totalwash and transfer buffer requirement was reduced by 1.000-fold in themicrofluidic system.

HIV Diagnosis from Human Sera.

Experiments were performed using the micro-Western as a HIV diagnosticassay for human sera. Typically, HIV diagnosis employs a conventionalwestern blot as the final (confirmatory) assay, following a positiveELISA-based screening result. In a 6-18 hr workflow, an HIV viral lysateis subjected to SDS-PAGE and immunoblotting (FIG. 21A). A 1:100 dilutionof patient serum is incubated with a nitrocellulose strip carrying theHIV protein bands. Any HIV-reactive antibodies in the serum bind tospecific HIV proteins on the strip. A positive result is indicated iftwo or more of the p24, gp41 and gp120/160 bands exhibit reactivity atleast as intense as that of the p24 band on a blotting strip subjectedto a weakly reactive control serum.

Experiments were performed using the micro-Western blot to assay humansera against purified gp120 and p24 HIV proteins (FIG. 21B). A mixtureof these antigens was subjected to the micro-Western assay, the laststep being probing of the immobilized antigens with 1:100 diluted humanserum. Specific serum reactivity to each “bait” protein was determinedusing a fluorescently labeled secondary antibody directed to human IgGon the separation medium. The resulting dose response was consistentwith the expected antibody titer in each of three serum samples(strongly reactive, weakly reactive, non-reactive); in accordance withthe U.S. Centers for Disease Control and Prevention guidelines fordetermining HIV infection in humans.

Materials and Methods

Microfluidic Assay Instrumentation.

Glass microchannels were functionalized with acrylate-terminatedself-assembled monolayers. The separation medium precursor contained7.5% w/v total acrylamide (7.5% T) with 2.7% of the total as thecrosslinker N,N′-ethylenebisacrylamide (2.7% C). BPMAC monomer was addedto precursor solutions at 3 mM from a 100 mM stock in DMSO (0.3 mol %with respect to acrylamides). BPMAC− precursors contained an equivalentvolume of DMSO lacking BPMAC. Gel precursor buffer was 37.5 mM tristitrated to pH 8.8 with HCl, 0.1% SDS, 0.1% Triton X-100. The initiatorsammonium persulfate (APS, 0.015%; A3678, Sigma-Aldrich, St. Louis, Mo.),N,N,N′,N′-tetramethylethylenediamine (TEMED, 0.05% v/v; T9281,Sigma-Aldrich) and riboflavin 5′ monophosphate (0.0006%; F1392,Sigma-Aldrich) were added just before introduction of degassed precursorto channels by capillary action. Separation gels and interfaces werephotochemically fabricated by 3 min chip exposure to a collimated blue(470 nm) LED source (M470L2, Thorlabs, Newton, N.J.) yielding ˜2.2 mWcm² at the chip plane for a 470 nm probe setting (LaserCheck lightmeter; 1098293, Coherent, Santa Clara, Calif.) through a custom chromephotomask (Photo Sciences Inc., Torrance, Calif.), followed by another 3min exposure step following exchange of gel precursor at access wellswith gel precursor buffer. Chemically fabricated gels did not requireblue light exposure, and were made similarly from precursors containing0.08% of each of APS and TEMED, but which lacked riboflavin.

Micro-Western Blot Protocol.

Samples were combined with a fluorescent molecular weight markercocktail in SDS-PAGE sample buffer (50 mM tris titrated to pH 6.8 withHCl, 2% SDS, 40 mM dithiothreitol), heated at 90° C. for 3 min, andloaded immediately after cooling to room temperature. Sample loading wasperformed electrophoretically at 100 V cm⁻¹ for 5 s. Sample was removedand the injection well filled with SDS run buffer containing glycine asa trailing ion for transient ITP (25 mM tris, 192 mM glycine, pH 8.3,0.1% SDS, 0.1% Triton X-100, 3% DMSO). Sample injection was performedunder constant-current conditions of 0.7 μA per well pair, producing avoltage ramp during SDS-PAGE from 50-350 V cm⁻¹ over a 60 s separationtime. SDS-PAGE was imaged in real time via a 4× epi-fluorescencemicroscope objective, voltage stopped and UV applied via the objectiveat ˜40 mW cm-2 for 45 s directly after separation was complete.Whole-channel green fluorescence imaging for marker proteins wasconducted under 10× magnification, prior to electrophoretic washing ofthe separation medium to remove uncaptured protein, 1 min each with SDSrun buffer and plain run buffer lacking SDS (25 mM tris, 192 mM glycine,pH 8.3, 0.1% Triton X-100, 3% DMSO) at 150 V cm⁻¹. Primary antibodyprobes were introduced in successive steps of electrophoretic loadingand washout from the separation medium, 20 min for each step at 150 Vcm⁻¹. Secondary antibodies were loaded and washed out for 10 min perstep. Antibodies were 100 nM each in plain run buffer (mixed in acocktail for multiplexed antigen detection) with 2 μM BSA for blockingpurposes (no separate gel blocking step was necessary). Final green andred fluorescence channel imaging was performed for marker proteins andMicro-Western blot probe readout respectively. Enzyme amplifieddetection was carried out via electrophoretic introduction offluorogenic DiFMUP phosphatase substrate (D6567, Invitrogen, Carlsbad,Calif.) at 600 V cm⁻¹, with blue DiFMU enzyme product imaged dynamicallyvia a UV-longpass filter cube under stopped-field conditions. DiFMUPfronts required <30 s to transit Micro-Western devices, with signaldevelopment observed over 10-30 s periods. Since DiFMU product was alsocharged, immobilized analyte bands could be assayed multiple times byremoving product electrophoretically between imaging cycles via 10 sfield pulses at 600 V cm⁻¹. For HIV serum assays, primary antibodysolution was replaced with 1:100 diluted serum in plain run buffer. Allother steps were performed as described.

Reagents and Samples.

BPMAC monomer was synthesized and verified by 1H NMR and massspectrometry as previously described in Example 1. Purified proteins,antibodies and fluorescence labeling protocols are described in Example1.

Data Acquisition and Analysis.

Whole channel imaging at 10× was conducted via stitching of adjacent,overlapping CCD images in ImageJ (NIH, Bethesda, Md.) to produce fullgel channel images and electropherograms.

Example 4 Microfluidic Separations for the Study of Molecule Switching

Introduction

Experiments were performed to study molecule switching duringseparations in microfluidic devices. In addition, experiments wereperformed to determine how specific protein mutations impact the coupledelectrostatic and photophysical properties of the fluorescent proteins.Physicochemical properties, such as isoelectric point, governed theseparations of molecules. When molecules switched states spontaneouslyor due to external stimuli, the properties governing the separationbehavior also changed, resulting in different separation patterns.Properties such as the switching rates, as well as underlying physicalmechanisms underlying the switching process were obtained from theseparation patterns.

Time-resolved microfluidic isoelectric focusing (IEF) and in situantibody blotting IEF were employed to monitor dark (non-fluorescent)and bright (fluorescent) protein populations of both wild-type Aequoreavictoria (av) green fluorescent protein (GFP) and the E222G mutantAequorea coerulescens (ac) GFP. Through IEF, each population wasobserved to exhibit distinct isoelectric points (pI) and, thus, distinctformal electrostatic charges. Interconversion between the dark andbright populations was controlled by differential exposure routines. Thestoichiometry and kinetics of charge transfer tied to this reversiblephotobleaching process were determined. In concert with areaction-transport model of bistable reversible charge and fluorescencephotoswitching, the on-chip measurements of population interconversionrates indicated that both rheostatic and discrete switch-like modulationof the electrostatic charge of the proteins depending on theillumination profile was possible. Additionally, it was estimated that3-4 formal charges distinguished the bright and dark populations ofavGFP, compared to one charge for those of acGFP. Given the proposedrole of E222 as a bridge between internal and exit hydrogen bondclusters within the GFP β-barrel, The difference in charge switchingmagnitude between the two mutants indicated the proton wire protontransport within the GFP structure, and proton exchange with the bulksolvent.

Experimental Procedures

Reagents and Materials

N-[3-[(4-Benzoylphenyl)formamido]-propyl]methacrylamide (BPMAC,C21H22N2O3, 350.2 g mol-1) monomer was synthesized via reaction of thesuccinimidyl ester of 4-benzoylbenzoic acid (323.3 g mol⁻¹; B1577,Invitrogen) with N-(3-aminopropyl)methacrylamide hydrochloride (178.7 gmol⁻¹; 21200, Polysciences, Warrington, Pa.) in the presence ofcatalytic triethylamine in dimethylformamide, purified, andcharacterized by 1H NMR and mass spectrometry. The monomer was added toBPMAC+ gel precursor solutions at 4.5 mM (˜1 mol % with respect toacrylamide) from a 100 mM stock in dimethylsulfoxide (DMSO) to imbueUV-induced protein photocapture functionality. BPMAC− precursors wereused in dynamic focusing experiments in which protein photocapture wasnot required and contained an equivalent volume of DMSO lacking BPMAC.

Purified recombinant wild-type GFP from Aequorea Victoria (avGFP) andthe Aequorea coerulescens E222G mutant (acGFP) were from Clontech(632373 and 632502, Mountain View, Calif.). Intact mass analysis of GFPisoforms was performed by high-resolution electrospray-ionization liquidchromatography-mass spectrometry in a Thermo LTQ Orbitrap XL instrumentat the QB3 Mass Spectrometry Facility at UC Berkeley. The primary goatpolyclonal antibody to GFP was prelabeled with Texas Red by themanufacturer (dye:protein molar ratio=2.9; ab6660, Abcam, Boston,Mass.). Equal volumes of a set of fluorescent IEF pI markers withabsorption maxima in the near-UV (pI 4.0, 4.5, 5.5, 6.2) were mixed in acocktail and added to GFP samples at 20× dilution (89827 and relatedproducts, Sigma).

Microfluidic Chip Fabrication

Microchannels were wet etched in optical white soda lime glass byCaliper Life Sciences (Hopkinton, Mass.). Each chip contained fourstraight-channel devices 10.4 mm in length, each consisting of threeparallel channels of 10 μm depth and 70 μm width between two 2 mmdiameter access wells providing fluidic interfacing via 10 μL press-fitpipet tips. Microchannels were functionalized with acrylate-terminatedself-assembled monolayers. Microfluidic gels were fabricated viaintroduction of a gel precursor solution by capillary action. Theprecursor contained 6% total acrylamide (6% T; % concentrations are w/vunless otherwise noted) with 2.6% of the total as the cross-linkerbisacrylamide (2.6% C), 15% v/v polybuffer 74 ampholytes (P9652, Sigma,St. Louis, Mo.), 0.1% v/v Triton X-100 detergent (T8532, Sigma), and 4.5mM BPMAC (see Reagents and Materials). The initiators ammoniumpersulfate (0.015%, A3678, Sigma), N,N,N′,N′-tetramethylethylenediamine(0.05% v/v, T9281, Sigma), and riboflavin 5′ phosphate (0.0006%, F1392,Sigma) were added just before introduction of degassed precursor tochannels. The precursor was polymerized by 6 min flood exposure of chipsto 470 nm blue light from a collimated LED source (M470L2, Thorlabs,Newton, N.J.) with access wells masked to restrict gelation to themicrochannels. The blue light intensity at a 470 nm probe setting was˜2.2 mW cm-2 at the chip plane, as measured by a LaserCheck light meter(1098293, Coherent, Santa Clara, Calif.). Equivalent isoelectricphotoswitching behavior was observed in gels chemically polymerized inthe absence of riboflavin.

Apparatus and Imaging

Chip imaging was conducted using an Olympus IX71 inverted fluorescencemicroscope equipped with an EMCCD camera (iXon3 885, Andor, Belfast,Northern Ireland), motorized stage (Applied Scientific Instrumentation,Eugene, Oreg.), and automated filter cube turret controlled throughMetaMorph software (Molecular Devices, Sunnyvale, Calif.). Illuminationwas provided by a mercury arc lamp mated to an automated shutter andattenuation system (X-Cite Exacte, Lumen Dynamics, Mississauga, ON,Canada). Electric field was applied via a custom high voltage powersupply built in-house. Gel photoimmobilization of proteins was conductedvia spot UV exposure through a 10× objective (Olympus UPIanFI, NA 0.3)and custom UV-long-pass filter cube (excitation 300-380 nm,emission >410 nm; XF1001, XF3097, Omega Optical) at ˜269 mW cm⁻² asmeasured via a 365 nm probe (UV513AB meter, General Tools, New York,N.Y.). The same cube was used to observe GFP under UV illumination alongwith fluorescent pI marker peptides, and channel positions were manuallyscored (gradient drift between focused-state marker and GFP isoformimaging steps was assumed to be negligible). Green and red fluorescencechannels were imaged at 10× using Omega Optical filter cubes optimizedfor GFP (XF100-3, excitation 445-495 nm at ˜89 mW cm⁻² for a 470 nmprobe setting, emission 508-583 nm) and DsRed2 (XF111-2, excitation525-555 nm, emission >575 nm). Whole channel imaging at 10×magnification was conducted via stitching of adjacent, overlapping CCDimages with 4×4 pixel binning in ImageJ (NIH, Bethesda, Md.) to producefull gel channel images and electropherograms. Imaging scans required˜20 s to complete. Real-time single-point imaging of GFP isoformdynamics was conducted in burst acquisition mode.

Transformation of fluorescence data via linear fits to pI markers andassociated data processing, including correction for constant cathodicisoform drift velocities in dynamic focusing experiments was performedusing MATLAB scripts written in-house (MathWorks, Natick, Mass.).Least-squares fitting of kinetic data was performed using gnuplotsoftware.

Chip Operation

After precursor gelation, gel access wells were flushed and replacedwith gel buffer consisting of precursor lacking monomers and initiators.Samples were made in gel buffer and introduced at loading wells (˜3 μLper well). Sample injection was performed at 200 V cm⁻¹ for 3 min.Opposing wells were briefly washed with catholyte (20 mM lysine, 20 mMarginine pH 10.1) and anolyte (70 mM phosphoric acid pH 1.4) andsubsequently filled. Focusing was conducted at 200 V cm⁻¹ for 2 minfollowed by 400 V cm⁻¹ for 1 min (focusing typically completed toequilibrium in 3 min or less). Imaging and UV photocapture steps (whereapplicable) were conducted individually for each device in series. UVphotocapture was conducted under floating (halted) electric field for 15s. Access wells were washed and filled with pH gradientmobilization/probe buffer consisting of 25 mM Tris, 192 mM glycine pH8.3, 0.1% v/v Triton X-100, and 3% v/v DMSO. Mobilization and washout ofpH gradients to the anodic wells was achieved via a 20 minelectrophoretic step. Fluorescently labeled anti-GFP antibody wasdiluted in probe buffer, loaded, and removed from gels in 20 minelectrophoretic steps. Probe loading and washout were conducted inopposite directions to minimize nonspecific signal remaining afterwashout. Finally, gels were scanned for captured GFP and antibodyfluorescence. Removal of the gel matrix after use was achieved byovernight incubation of the chip in a 2:1 solution of 70% perchloricacid and 30% hydrogen peroxide heated to 75° C., allowing efficientrecycling of glass chips

General Utility and Demonstrated Applications

Using dynamic IEF, dark (non-fluorescent) and bright (fluorescent)populations of avGFP and acGFP were observed and characterized bymeasuring changes in protein fluorescence and pI (FIG. 22). After IEF,an immunoblotting step was performed so that non-fluorescent analytescould be detected. Incubation of fluorescently labeled antibodies withIEF-resolved- and immobilized-proteins yielded pI and mass distributionfor each target, including non-fluorescent forms of GFP. To immobilizeproteins, IEF was performed in a light responsivebenzophenone-decorated, polyacrylamide gel (light-activatedvolume-accessible separation gel). Brief exposure of the gel to UV lightcovalently attached proteins to the gel matrix, allowing subsequentprotein probing via introduction of fluorescently labeled antibodies.The ability to blot and probe proteins with near-lithographic spatialcontrol in direct series with controlled light pre-exposure sequencesenabled quantitation in the absence of an endogenous fluorescence signalfrom the protein target. In the case of GFP, immunoblotting corroboratedpI photoswitching measurements inferred from intrinsic fluorescencedata. The GFP fluorescence signals had complex dependencies on lightexposure history and chemical environment.

IEF analysis yielded three predominant isoforms for each variant in thepI 4.8-5.5 range under continuous blue light excitation (isoforms weredenoted α, β and γ for avGFP; and δ, ε and ζ for acGFP) (FIG. 23). Theseheterogeneous isoform patterns were ascribed to differential C-terminalcleavage by non-specific proteases during bacterial expression of therecombinant proteins. This difference was consistent with cleavage ofthe C-terminal lysine in the a isoform of avGFP. Given that the cleavedlysine residue contributed a full positive charge, the pI shiftattributable to a single electrostatic charge was estimated at roughly0.12-0.15 pH units from the relative bright isoform displacements in thepH axis of FIG. 23, and from further computational estimation of theexpected isoform pls resulting from differential C-terminal cleavage(data not shown). Thus, the magnitudes of isoelectric pointphotoswitching were calibrated using a ruler of electrostatic charge toallow direct inference of the stoichiometry of charge transfer events atsingle-charge resolution. The effect of charge transfer on the pI of aprotein via its titration behavior had complex dependencies on, forexample, the pI itself, and the molecular weight and amino acidcomposition of the protein. Thus, this “charge ruler” approximation wasused under the assumption that the pI range over which charge shifts areestimated was narrow enough to assume a constant local slope in thecharge vs. pH titration curve of the isoforms considered.

Experiments were performed to investigate the effect of UV and bluelight illumination on avGFP and acGFP isoform distributions duringdynamic IEF. For both avGFP and acGFP, isoforms exhibited dynamicchanges in isoelectric point distributions upon exposure of the focusedproteins to sequences of UV and blue light illumination (FIG. 24). Tosummarize the observed photoswitching phenomena: brief exposure of thefocused fluorescent isoform bands to UV light induced formation of dark(reversibly bleached) isoform populations with increased pI compared tobright isoforms (FIGS. 23-25). Following UV exposure, application ofblue illumination initiated a dynamic “switch-on” of the fluorescence ofthe dark isoforms with first-order time constants of 700 ms for avGFPand 720 ms for acGFP (FIG. 24(A)). Concomitantly, migration of theswitched-on isoforms to the pls of their “parent” bright isoforms wasobserved on a ˜5-10 s timescale. More prolonged exposure to UV on thefocusing timescale caused a transient increase in the apparent pls ofbright isoforms to values intermediate between the static bright anddark isoform pls. This apparent bright isoform pI increase reversed whenUV illumination was halted (FIG. 24(B)), while dark isoforms assumedtheir higher pls until blue light was applied (or until the darkisoforms relaxed back to the bright state during prolonged nilillumination).

Measurement of the dark isoform peak areas as a function of UVpre-exposure time revealed single-exponential switch-off kinetics with atime constant of 67 ms. This kinetic approximately matched the fastbleaching time constant of 56 ms under direct UV exposure of avGFP (FIG.25 (B)). These results indicated that reversible bleaching of bright GFPisoforms by UV exposure was the trigger for formation of dark stateisoforms with alkaline-shifted pls. The dark isoform populations,constituting ˜25% of the total mass for avGFP after ≳150 ms UV exposure,also decayed back to the bright state under nil illumination conditions(FIG. 25(C)). The relatively short ˜5-10 s focusing timescale (comparedto the characteristic time of dark population decay) enabled resolutionof dark from bright populations. This decay process was again describedby single-exponential kinetics, with a time constant of 42.2 s foravGFP, which was similar to literature values of 58 and 54 s measured inmammalian cells for ECFP and EYFP respectively. Thus, blue photonabsorption reduced the fluorescence switch-on time of reversiblybleached dark isoforms by a factor of ˜60-fold (from 42 to 0.7 s) underthe experimental conditions employed.

The distributions of the photoswitched isoforms may be related to thecharge transfer events underlying the changes in isoelectric point. Twomutant-specific differences in these focusing behaviors were observedfor avGFP and acGFP. Firstly, prolonged application of UV light causedapparent pI shifts of 0.12 and 0.10 units for all bright avGFP and acGFPisoforms respectively, as well as broadening of the focused zone bandwidths (4σ) by 2.47- and 1.24-fold respectively (as measured for themajor β and ε isoforms, FIG. 24(B)). Secondly, the final pI shifts ofeach of the dark isoforms (e.g., β′) from their parent bright bands(e.g., β) after halting illumination were ˜0.45 and ˜0.15 pI units foravGFP and acGFP respectively (˜3-4 and ˜1 charge units, FIG. 23). Thefact that these bright-to-dark pI shifts were discrete, rather thanspread over a distribution, indicated an all-or-nothing conversionprocess. Thus, the GFPs exhibited a bistable switch with respect to pI(at least on the fluorescence timescale) and with respect tofluorescence.

The GFP bistable switching was studied by modeling the isoelectricphotoswitching of the predominant avGFP isoform between bright (β) anddark (β′) states having distinct pls. GFP molecules interconvertedbetween these states according to an equilibrium reaction of the form β

β′ with forward and backward rate constants of k_(β→β′) and k_(β′→β)respectively. The rate constants were determined by least squaresfitting of the equilibrium bright population distributions obtained fromthe model to experimentally measured distributions. Focused avGFPisoform distribution fits were made across a range of UV illuminationintensities. Governing equations for this model considered focusing anddiffusive spreading of peaks (terms 1 and 2 on the right hand side ofeach equation), as well as first-order interconversion of bright anddark populations (terms 3 and 4):

$\begin{matrix}{\frac{{dC}_{\beta}}{dt} = {{{p_{\beta}\left( {x - x_{{pI},\beta}} \right)}E_{x}\frac{{dC}_{\beta}}{dx}} + {D_{\beta}\frac{d^{2}C_{\beta}}{{dx}^{2}}} - {k_{\beta\rightarrow\beta^{\prime}}C_{\beta}} + {k_{\beta^{\prime}\rightarrow\beta}C_{\beta^{\prime}}}}} & (1) \\{\frac{{dC}_{\beta^{\prime}}}{dt} = {{{p_{\beta^{\prime}}\left( {x - x_{{pI},\beta^{\prime}}} \right)}E_{x}\frac{{dC}_{\beta^{\prime}}}{dx}} + {D_{\beta^{\prime}}\frac{d^{2}C_{\beta^{\prime}}}{{dx}^{2}}} - {k_{\beta^{\prime}\rightarrow\beta}C_{\beta^{\prime}}} + {k_{\beta\rightarrow\beta^{\prime}}C_{\beta}}}} & (2)\end{matrix}$Where C is concentration, t is time, x is distance along the separationaxis, p_(β)≈p_(β′)=p is slope in analyte mobility with respect to x, Eis applied electric field, and D_(β)≈D_(β′)=D is the diffusivity of GFPin the separation gel. Non-dimensionalization of the model with respectto the characteristic diffusion time between population peaks (Δx_(pI)²/D) yielded three parameters 1) a Peclet number Pe=pΔx_(pI) ²E_(x)/D,the ratio of diffusive and convective (focusing) timescales, 2) aDamkohler number κ=k_(β→β′)Δx_(pI) ²/D, the ratio of diffusive andforward reaction timescales, and 3) an equilibrium constantγ=k_(β′→β)/k_(β→β′), the ratio of backward and forward reaction rates.

The dimensional analysis in FIG. 26(A) shows the diverse behavior ofthis convection-diffusion-reaction model. The reaction:focusing speedratio κ/Pe and the equilibrium constant γ divide the (k_(β→β′),k_(β′→β)) parameter space into several behavioral regimes that weredirectly mapped onto experimental data. At low UV intensities (κ/Pe<1),the bright and dark populations interchanged slowly enough compared tothe focusing timescale that distinct bright and dark peaks were formed,producing a wide overall concentration distribution in the pI axis. Asthe UV intensity increased, the populations interchanged more rapidly,and the rate constants k_(β′→β) and k_(β→β′), increased at anapproximately fixed ratio over the intensity range studied (γ˜2.9, FIGS.26(B) and (C)). Rapid interconversion caused the observed bright anddark distributions of the major avGFP isoform to converge along the pIaxis at a weighted mean pH of 5.12 at (pI_(β′)−pI_(β))/(1+γ)=0.12 pHunits from pI_(β)=5.00, since γ=C_(β)/C_(β′), at equilibrium. The 5-270mW cm⁻² range in UV intensity studied produced an intensity-independentequilibrium in which each GFP molecule was bright with pI 5.00 around74% of the time, and dark with pI 5.45 around 26% of the time.Increasing the UV intensity reduced the average time spent by a moleculein each state between switching events. Increases in each rate constant,and thus κ/Pe, accounted for the transitions in shape (wide to narrow)and position (lower pI to higher pI) of the observed bright isoformdistributions, since the ability to resolve the bright and darkpopulations by focusing decreased as populations interconverted more andmore rapidly.

Dynamic analysis over lower intensity ranges was limited by detectionsensitivity, given that the GFP stimulation and imaging conditions wereone and the same. Under nil illumination conditions, only the brightisoform populations existed (FIG. 23), which indicated a transition tothe γ_(avGFP) 2.9 equilibrium over the 0-5 mW cm⁻² UV intensity rangeand the ability to manipulate the mean avGFP pI from 5.00-5.12 in arheostatic fashion. Similar fitting of experimental data for acGFP wasconfounded owing to a low fluorescence SNR caused by the heavily reducedUV absorbance in E222G mutants. However, assuming that the simpletwo-state model also holds for acGFP, the equilibrium brightdistribution pI shift of 0.1 units at 100% UV yields γ_(acGFP)˜0.5 atmost, meaning that at least 67% of the acGFP was in the dark state atequilibrium.

The photophysics of the family of green fluorescent proteins derivedfrom Aequorea sp. are characterized by an interconnection betweenspectral properties and short and long-range proton dynamics involvingtheir chromophores. The diversity of photophysical characteristics ofthe fluorescent proteins indicate a complex interconnection betweenpH-dependent and -independent protonation equilibria, proton exchangewith the bulk solvent ENREF 51, chromophore and pocket residueconformation, electrostatic interactions between the chromophore andsurrounding residues in the chromophore pocket, and irreversiblechemical reactions at the chromophore or surrounding residues; all ofwhich contribute to the divergent absorption, emission, photoactivationand reversibility aspects of the fluorescence of GFP family members.

Experiments were performed to study the UV intensity-dependent IEFfocusing behavior of GFP isoforms at the ensemble level by determiningthe interplay between reaction and transport timescales. Specific to theGFP studies conducted here, the wild type Aequorea victoria avGFP, aβ-barrel structure containing a buried tripeptide chromophore formedautocatalytically from Ser65, Tyr66 and Gly67, exhibited fluorescencewith absorption bands at both ˜400 and ˜475 nm. These absorption bandsincluded two subpopulations A and B having, respectively, neutral(protonated) and anionic (deprotonated) charge at the hydroxyl group ofTyr66 of the buried chromophore. While the neutral A form dominated B by6:1 in wild-type avGFP, S65T (e.g., EGFP) and E222G (e.g., acGFP, amodified GFP from Aequorea coerulescens) mutants favored the anionic Bstate in the physiological pH range, thus suppressing the 404 nmabsorption peak and simplifying their photophysical behavior. Picosecondspectroscopy studies indicated an excited-state proton transfer (ESPT)process that occurred upon excitation of the protonated A state, whichcaused the phenolic proton at Tyr66 to delocalize and transfer to Glu222via a network of hydrogen bonds due to a drop in the pK_(a) of thetyrosyl phenol in the excited state.

The isoelectric point photoswitching in avGFP indicated the arrangementof the switching wavelengths (higher energy light shifts equilibriumtowards dark state; lower energy light hastens fluorescence recovery),kinetic parameters, and GFP variants studied. The P and B_(r)fluorescence states were characterized by distinct electrostatic chargestates at the whole molecule level via direct physicochemicalmeasurement with dynamic IEF. These distinct electrostatic charge statesindicated proton exchange with the bulk solvent. The polarity of theobserved pI shifts further indicated that the transition of GFPs to thedark state involved proton uptake into their structures (causingincreased pI), and vice versa, that the return to the bright stateinvolved expulsion of protons (causing decreased pI). Thus, theobservations of single-charge resolution pI indicated that at least oneproton uptake event occurred for the P to B_(r) transition, although thespecific residue(s) involved in this process were not identified via thewhole molecule-level measurements of electrostatic charge made here.However, the observed difference in protonation stoichiometry betweenavGFP and acGFP may indicate structural rearrangements underlying thereversible bleaching process.

Specifically, the all-or-nothing uptake of 3-4 protons by avGFP isoformsduring fluorescence switch-off may indicate a cascade of rearrangementsin the proposed internal hydrogen bonding network buried within theavGFP structure extending from the chromophore pocket beyond the E222bridge. For example, there may be multiple proton storage within the GFPstructure at buried hydronium ions and titratable residues. Given thatproton travel between the proposed internal and exit hydrogen bondclusters was expected to be restricted or rerouted by the E222G mutationin acGFP, the single-charge shift between bright and dark statesobserved for the acGFP isoforms may result from titration dynamicsrestricted to the chromophore pocket that were facilitated byacid-induced protonation of a pocket residue that governs transitionbetween the bright P and dark B_(r) states.

Although the foregoing embodiments have been described in some detail byway of illustration and example for purposes of clarity ofunderstanding, it is readily apparent to those of ordinary skill in theart in light of the teachings of the present disclosure that certainchanges and modifications may be made thereto without departing from thespirit or scope of the appended claims. It is also to be understood thatthe terminology used herein is for the purpose of describing particularembodiments only, and is not intended to be limiting, since the scope ofthe present invention will be limited only by the appended claims.

Where a range of values is provided, it is understood that eachintervening value, to the tenth of the unit of the lower limit unlessthe context clearly dictates otherwise, between the upper and lowerlimit of that range and any other stated or intervening value in thatstated range, is encompassed within the invention. The upper and lowerlimits of these smaller ranges may independently be included in thesmaller ranges and are also encompassed within the invention, subject toany specifically excluded limit in the stated range. Where the statedrange includes one or both of the limits, ranges excluding either orboth of those included limits are also included in the invention.

All publications and patents cited in this specification are hereinincorporated by reference as if each individual publication or patentwere specifically and individually indicated to be incorporated byreference and are incorporated herein by reference to disclose anddescribe the methods and/or materials in connection with which thepublications are cited. The citation of any publication is for itsdisclosure prior to the filing date and should not be construed as anadmission that the present invention is not entitled to antedate suchpublication by virtue of prior invention. Further, the dates ofpublication provided may be different from the actual publication dateswhich may need to be independently confirmed.

It is noted that, as used herein and in the appended claims, thesingular forms “a”, “an”, and “the” include plural referents unless thecontext clearly dictates otherwise. It is further noted that the claimsmay be drafted to exclude any optional element. As such, this statementis intended to serve as antecedent basis for use of such exclusiveterminology as “solely,” “only” and the like in connection with therecitation of claim elements, or use of a “negative” limitation.

As will be apparent to those of skill in the art upon reading thisdisclosure, each of the individual embodiments described and illustratedherein has discrete components and features which may be readilyseparated from or combined with the features of any of the other severalembodiments without departing from the scope or spirit of the presentinvention. Any recited method can be carried out in the order of eventsrecited or in any other order which is logically possible.

Accordingly, the preceding merely illustrates the principles of theinvention. It will be appreciated that those skilled in the art will beable to devise various arrangements which, although not explicitlydescribed or shown herein, embody the principles of the invention andare included within its spirit and scope. Furthermore, all examples andconditional language recited herein are principally intended to aid thereader in understanding the principles of the invention and the conceptscontributed by the inventors to furthering the art, and are to beconstrued as being without limitation to such specifically recitedexamples and conditions. Moreover, all statements herein recitingprinciples, aspects, and embodiments of the invention as well asspecific examples thereof, are intended to encompass both structural andfunctional equivalents thereof. Additionally, it is intended that suchequivalents include both currently known equivalents and equivalentsdeveloped in the future, i.e., any elements developed that perform thesame function, regardless of structure. The scope of the presentinvention, therefore, is not intended to be limited to the exemplaryembodiments shown and described herein. Rather, the scope and spirit ofpresent invention is embodied by the appended claims.

That which is claimed is:
 1. A method of assaying molecule switching,the method comprising: separating a sample comprising a molecule using amicrofluidic device to obtain a separation pattern, wherein themicrofluidic device comprises a separation medium comprising functionalgroups that covalently bond to the molecule upon application ofelectromagnetic radiation and the method further comprises applying theelectromagnetic radiation to the separation medium to covalently bondthe molecule to the separation medium; detecting a first separationpattern of the molecule in a first state of a switching characteristicof the molecule; applying an external stimulus to the molecule such thatthe molecule changes from the first state of the switchingcharacteristic to a second state of the switching; detecting a secondseparation pattern of the molecule in the second state of the switchingcharacteristic of the molecule; and determining a change between thefirst separation pattern and the second separation pattern to assay theswitching characteristic of the molecule.
 2. The method according toclaim 1, further comprising contacting the separation medium with alabel that specifically binds to the molecule covalently bound to theseparation medium.
 3. The method according to claim 2, furthercomprising detecting the label.
 4. The method according to claim 3,wherein the label comprises a labeled antibody.
 5. The method accordingto claim 1, wherein the molecule is a protein.
 6. The method accordingto claim 5, wherein the protein is a fluorescent protein.
 7. The methodaccording to claim 6, wherein the switching characteristic is aphotoswitching characteristic.
 8. The method according to claim 7,wherein the photoswitching characteristic is a change betweenfluorescent and non-fluorescent states.
 9. The method according to claim8, wherein the method includes determining a rate of photoswitchingbetween fluorescent and non-fluorescent states.
 10. The method accordingto claim 8, wherein the method includes determining a mechanism ofphotoswitching between fluorescent and non-fluorescent states.
 11. Themethod according to claim 1, wherein the sample is microfluidicallyseparated using an equilibrium separation technique.
 12. The methodaccording to claim 11, wherein the equilibrium separation techniquecomprises isoelectric focusing.
 13. The method according to claim 1,wherein the sample is microfluidically separated using a non-equilibriumseparation technique.
 14. The method according to claim 13, wherein thenon-equilibrium separation technique comprises gel electrophoresis. 15.The method of claim 1, wherein determining a change between the firstseparation pattern and the second separation pattern comprisesdetermining a kinetic property of the switching characteristic of themolecule.
 16. The method of claim 1, wherein determining a changebetween the first separation pattern and the second separation patterncomprises determining a mechanism of the switching characteristic of themolecule.
 17. The method of claim 1, wherein the microfluidic devicecomprises an elongated flow path.
 18. The method of claim 17, whereinthe separation medium comprises a polymeric gel substantially filling aninterior volume of the elongated flow path after application ofelectromagnetic radiation such that the sample comprising the moleculetraverses the separation medium as the sample flows through theelongated flow path.
 19. A system for assaying molecule switching, thesystem comprising: (a) a microfluidic device comprising a separationmedium configured to separate a sample comprising a molecule to obtain aseparation pattern, wherein the separation medium comprises functionalgroups that covalently bond to the molecule upon application ofelectromagnetic radiation and the system is configured to apply theelectromagnetic radiation to the separation medium to covalently bondthe molecule to the separation medium; and (b) a processor programmed todetermine a switching characteristic of the molecule from a changebetween a first separation pattern and a second separation pattern ofthe sample, wherein the system is further programmed to: detect a firstseparation pattern of the molecule in a first state of the switchingcharacteristic of the molecule; apply an external stimulus to themolecule such that the molecule changes from the first state of theswitching characteristic to a second state of the switchingcharacteristic; detect a second separation pattern of the molecule inthe second state of the switching characteristic; and determine a changebetween the first separation pattern and the second separation patternto assay the switching characteristic of the molecule.
 20. The systemaccording to claim 19, further comprising a source of electromagneticradiation.
 21. The system according to claim 20, wherein theelectromagnetic radiation source is a light source.
 22. The system ofclaim 19, wherein the microfluidic device comprises an elongated flowpath.
 23. The system of claim 22, wherein the separation mediumcomprises a polymeric gel substantially filling an interior volume ofthe elongated flow path after application of electromagnetic radiationsuch that the sample comprising the molecule traverses the separationmedium as the sample flows through the elongated flow path.
 24. A kitcomprising: (a) system for assaying molecule switching according toclaim 19; and (b) a buffer.